I doubt that there is a way to have> 2011/6/29 Gianluca Interlandi <gianluca_at_u. 0 and 2. washington. At the point of breaking the temperature raises of a few> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. From: Gianluca Interlandi (gianluca_at_u. The server where VMD is started from has On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. Gianluca Interlandi Research Assistant Professor. " >> Could a small damping coefficient lead to such errors? If so, what would >> be the scenarioGianluca On Sun, 30 Aug 2009, Axel Kohlmeyer wrote: > On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: >> Thank you Mike for sharing your information. I have to run following commands 2 times in tcl. >> >> i am attaching some graphs with performance numbers from. uiuc. In the text field you can enter your atom selection, e. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. edu> > wrote: > are other people also using those GPUs? > >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi <gianluca_at_u. edu> > wrote: > Roy, > > I think that you are confusing two things. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. Re: Abe versus Lincoln. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. I would be > happy if somebody could point me out to some scripts which help me performOn Thu, 5 Apr 2012, Gianluca Interlandi wrote: > What is the advantage of the multicore version of charm++ versus net-linux? > Is multicore faster if I'm running for example on a 32-core magny-Cours AMDFrom: Gianluca Interlandi (gianluca_at_u. Gianluca Interlandi, ‡, 1, 2 Olga Yakovenko, ‡, 1 An-Yue Tu,. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. Author Profile. Interlandi et al. SMD on center of mass. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2. 15 K 1 KT = 2. During the minimization and equilibriation with protein constrained, the > disulfide bond breaks. washington. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). how to output more significant figures in a file for energies and forces? Next message: Gianluca Interlandi: "Re: accuracy of measurement"Locking up the spike protein to prevent infection. edu) Date: Thu Apr 09 2015 - 17:39:49 CDT Next message: Gianluca Interlandi: "Re: measure sasa not consistent" Previous message: John Stone: "Re: measure sasa not consistent" Next in thread: Gianluca Interlandi: "Re: measure energy"> From: Gianluca Interlandi [gianluca_at_u. 6 : Tue Dec 27 2016 - 23:21:14 CST Gianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. You should simulate it in explicit water (or try one of the implicitGianluca Interlandi is on Facebook. The more tasks you have the > more frequently the CPUs need to update each other about the position > of Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Reply: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Reply: Axel Kohlmeyer: "Re: Fwd: Installing NAMD on windows" Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. Next in thread: Gianluca Interlandi: "Re: Should you cap C and N termini?" Reply: Gianluca Interlandi: "Re: Should you cap C and N termini?" Messages sorted by: [ attachment ] We generally use caps because our systems are individual domains within larger proteins. I doubt that there is a way to have NAMD output theReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. uiuc. washington. " Previous message: Gianluca Interlandi: "multicore vs ibverbs" Messages sorted by: [ attachment ] Dear NAMD list, I am a bit. . edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallNext in thread: Gianluca Interlandi: "Re: NAMD 2. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message:. Gianluca Interlandi , Contributed equally to this work with: Pavel Aprikian, Gianluca Interlandi Affiliation Department of Bioengineering, University of Washington, Seattle, Washington, United. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. Policies. This school has it's > own biophysics division. MyGianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. washington. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallYesterday at about 11:45 a. edu> wrote:Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. This is unrelated to KDE3. It's > slightly faster but still not that much faster than running on 16 CPU cores. washington. View Gianluca Interlandi’s profile on LinkedIn, the world’s largest professional community. edu) Date: Thu Nov 02 2006 - 13:55:24 CST Next message: Ugur Akgun: "ABF on a single molecule" Previous message: Al-Rawi, Ahlam: "external force" In reply to: Al-Rawi, Ahlam: "external force" Next in thread: Gianluca Interlandi:. >> >> i am attaching some graphs with performance numbers from. Katrina T. I did what you and Gianluca suggested but still have two caveats. That's why one wants to use a low value for the damping constant, in principle. Juli 2012 00:26 > An: Aron Broom > Cc: NAMD list > Betreff: Re: namd-l: Running NAMD on Forge (CUDA) > > Yes, I was totally surprised, too. You should simulate it in explicit water (or try one of the implicitGianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. Choose File -> Save Coordinates. edu> wrote: > Hi Fatemeh, > > Thanks for replying. What are you trying to accomplish? Previous message: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" In reply to: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" Next in thread: Axel Kohlmeyer: "Re: SSD vs SSHD vs mechanical" Messages sorted by: [ attachment ] At present I don't think NAMD will let you write a js Next in thread: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Gianluca: Using VMD with the attached script should solve that. I would be > happy if somebody could point me out to some scripts which help me perform Hemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. Join Facebook to connect with Gianluca Interlandi and others you may know. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". washington. edu) Date: Mon Oct 11 2010 - 16:56:03 CDT Next message: Basak Isin: "Re: Regarding answering questions in a forum. washington. Sunhwan On Jul 16, 2014, at 12:32 AM, Gianluca Interlandi <gianluca_at_u. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. On 6 May 2009, at 11:04, Gianluca Interlandi wrote: > Thanks Anton for your answer. washington. Re: Vibrational mode analysis. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. Re: Protein in/out of box. In reply to: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] How would somebody want to simulate explicit water molecules without PBC? The water molecules will quickly diffuse and your protein be in vacuum. org/0000-0001-5445-9587; Department of Bioengineering, University of Washington, Seattle, Washington. 85. These are the lastIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. 5923 Kcal/mol also we have 6. washington. 97 pN*nm = 1 Kcal/molIn reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. I > would be happy if somebody could point me out to some scripts which help me > perform that. edu> > wrote: > Roy, > > I think that you are confusing two things. washington. Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. washington. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. edu) Date: Wed Jun 15 2011 - 14:18:43 CDT Next message: Reichert, David: "RE: Question about equilibration" Previous message: Richard Wood: "Re: Question about equilibration" In reply to: Richard Wood: "Re: Question about. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you canThe bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. > From: Gianluca Interlandi [gianluca_at_u. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Re: NAMD 2. I would be > happy if somebody could point me out to some scripts which help me performRe: Help building a desktop for namd. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. washington. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in understanding at molecular level the function of proteins involved in hemostasis and thrombosis, and how they interact with each other and with material surfaces. washington. 5923 Kcal/mol also we have 6. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). edu]Reply All Saturday,. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthRe: NAMD 2. 7 On Wed, Sep 18, 2013 at 11:43:49AM -0700, Gianluca Interlandi wrote: > Dear VMD list, > > I think that this question was asked previously. 6 ns/day for a 100k atom system with roughly those same parameters (and. >Re: Vibrational mode analysis. NAMD doesn't that i know of. Eric Klavins Professor. PMID: 33550613 PMCID: PMC8089038 DOI: 10. uiuc. Policies. The otherGianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. Forest, Academic Editor. washington. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. In the text > field you can enter your atom selection, e. 6 version, although I am not running the cluster at full load yet. Managing Member/Principal Atlantic Mortgage Partners, LLC Jun 2009 - Jun 2012 3 years 1. 7b1 - effects of configuration parameters and hardware. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. Previous message: Gianluca Interlandi: "NAMD 2. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. MyFrom: Gianluca Interlandi (gianluca_at_u. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. edu> wrote: > Hi Fatemeh, > > Thanks for replying. washington. washington. washington. edu > <mailto:gianluca_at_u. washington. washington. E-mail: [email protected] > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. (2010) The catch bond mechanism between von Willebrand factor. Cancellation policy. 7b4 is thatRE: DCD. > > Forget about creating a pdb file. edu> > wrote: > are other people also using those GPUs? > > > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi! Next in thread: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Gianluca: Using VMD with the attached script should solve that. washington. From: Victor Kwan (vkwan8_at_uwo. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. washington. washington. Kid friendly. washington. uiuc. Next in thread: Gianluca Interlandi: "Re: NAMD 2. g. View the profiles of professionals named "Gianluca Interlandi" on LinkedIn. edu> > wrote: From: Gianluca Interlandi [gianluca_at_u. There have been over 180 downloads and no complaints so far. From: Gianluca Interlandi (gianluca_at_u. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. I was getting 2. Display options Format Abstract The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. Reply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. The energy term mustOn Mon, 11 Apr 2011, Gianluca Interlandi wrote: > Salvador, > > You might also want to apply for computing time at one of the national > supercomputing centers through Teragrid. edu) Date: Tue Oct 03 2006 - 00:01:37 CDT Next message: Ugur Akgun: "SMD From Force to Free Energy" Previous message: JC Gumbart: "Re: How can I do protein complex's simulation?" In reply to: Gianluca Interlandi: "SMD and. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. 5923 Kcal/mol also we have 6. From: Gianluca Interlandi (gianluca_at_u. washington. edu) Date: Thu Sep 21 2006 - 16:55:46 CDT Next message: jonathan_at_ibt. edu on behalf of Gianluca Interlandi [gianluca_at_u. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi <gianluca_at_u. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. Gianluca On Sun, 30 Aug 2009, Gianluca Interlandi wrote: > Thanks Axel, > > I have also compared the cost of a GPU equiped PC versus a dual Quadcore PC. washington. Bathrooms: 1. washington. In reply to: Gianluca Interlandi: "Re: Force field design" Next in thread: Axel Kohlmeyer: "Re: Force field design" Reply: Axel Kohlmeyer: "Re: Force field design" Messages sorted by: [ attachment ] On 24 July 2014 22:22, Gianluca Interlandi <gianluca_at_u. washington. edu> wrote: >> if you want to go low risk and don't have much experience with GPU, then >> probably the best deal you can currently get for running. From: Victor (ovchinnv_at_gmx. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallOn Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. washington. Search for: Main Menu. You should simulateCorresponding Author. edu> wrote: > I'm cc'ing here the NAMD list so that others. washington. The simulations were not performed at constant velocity > but at constant force. double. But if you simulate entire proteins, charged termini. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" In reply to: Gianluca Interlandi: "Re: NAMD 2. From: Gianluca Interlandi (gianluca_at_u. Hope the video helps, but now I'm embarrassed. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in. Usually, this > is > written in the dcd file if you specified "DCDUnitCell yes" in your > NAMD > config file. 7 released. uiuc. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread: Maxime Boissonneault: "Re: namd ibverbs" The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the charmm++. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. On Tue, Jul 10, 2012 at 1:14 PM, Gianluca Interlandi < gianluca_at_u. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. washington. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. From: Gianluca Interlandi (gianluca_at_u. Name : Current Position : Tim Connolley, Bioengineering 2005 : Michigan State Mechanical Engineering Graduate Program: Brett Anderson, Bioengineering 2006Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthCorrespondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. 7 ns/day, which seems decent given the system size. edu] Sent: Monday, June 20, 2016 12:46 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. Display options. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. Is it appropriate to use a > >thermostat and barostat (CPT) while performing a constant force orRe: Force field design. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. October 10, 2019 - Present·Syracuse, Italy Da Host fai da te a Imprenditore Extra Alberghiero Owner and Founder at Baroque Apartments Syracuse, Italy Agenzia di affitti. > On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > > > Dear Marcos, > > > > Thanks a lot for your answer and for offering me your help. PMID: 37700555; DOI: 10. VMD-L Mailing List. washington. washington. washington. washington. The simulations were not performed at constant velocity > but at constant force. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. Semantic Scholar's Logo. Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. In the NAMD folder that you downloaded there >> is a file called "notes. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. edu> wrote: > Hi Fatemeh, > From: Gianluca Interlandi (gianluca_at_u. washington. washington. washington. There have been over 180 downloadsGianluca Interlandi, Wendy Thomas, The catch bond mechanism between von Willebrand factor and platelet surface receptors investigated by molecular dynamics simulations, "Proteins: Structure, Function, and Bioinformatics",. Just source the Tcl file and use the 'unwrap' procedure. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" From: Gianluca Interlandi (gianluca_at_u. On Tue, 14 Dec 2004, Gianluca Interlandi wrote: > Dear NAMD users, > > I have two independent questions: > > 1) Are there any experiences about the scalability running NAMD on > infiniband? I have been running NAMD on myrinet and, as an example, for > a system with 51000 atoms I get a seedup of 14 on 16 CPUs (dual opteron > 1800+). edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. g. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. edu> > wrote: > are other people also using those GPUs? > >Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] kcal/mol/A^2 is actually units for a force constant (for a spring for. NAMD supports CHARMM22 parameter files. Next message: Gianluca Interlandi: "Infiniband and PME gridsize" Previous message: nordgren_at_sas. However, using monoclonal antibodies specific for the mannose-binding Escherichia coli. > > According to your banchmarks, it looks like the less expensive GTX285. My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Mon, Aug 26, 2013 at 12:56 PM, Gianluca Interlandi < gianluca_at_u. > > NCSA Forge has for example 6 CUDA devices and 16 CPU cores per node. washington. edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. coli UTI89 on mannan-coated surfaces and bladder infection in mice. washington. eduRe: Question about equilibration. com) Date: Thu Apr 07 2011 - 14:21:33 CDT Next message: Gianluca Interlandi: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Gianluca Interlandi: "Re: Abe versus Lincoln" Next in thread: Gianluca Interlandi: "Re:. Eric Klavins Professor. Be the first to write a review. We are building a smaller cluster though in the lab and will test the scalability2006/9/6, Gianluca Interlandi <gianluca_at_u. In reply to: Gianluca Interlandi: "Compiling NAMD 2. The Bacterial Fimbrial Tip Acts as a Mechanical Force Sensor. You simply load your trajectory > into VMD Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. Maybe the file was not transferred correctly to your desktop PC. /night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum stay: 2 night(s) Book online - Book holiday rental 11131246 with Vrbo. I got 0. > On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. edu> Date: Friday, May 4, 2007 6:53 pm Subject: Re: namd-l: query about wrapped coordinates > This script needs the information about the box size. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"UW Bioengineering is pleased to announce the hires of faculty Barry Lutz and Gianluca Interlandi, as well as the promotion of Suzie Pun to full professor. edu> wrote: > Hi Fatemeh, >> On Wed, Dec 12, 2012 at 12:26 PM, Gianluca Interlandi <gianluca_at_u. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"> On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. Gianluca Interlandi 1 , Minhua Ling, An Yue Tu, Dominic W Chung, Wendy E Thomas Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, United States of America. washington. ch>: > Hi Nathalie, > > It seems that CHARMM doesn't read the residue number correctly: > > 2011/6/29 Gianluca Interlandi <gianluca_at_u. Bioengineering. edu) Date: Wed Sep 29 2010 - 16:34:24 CDT Next message: Gianluca Interlandi: "Re: Re: Experience with Asus Netbook" Previous message: TRINH Minh Hieu: "Re: Re: Experience with Asus Netbook" In reply to: TRINH Minh Hieu: "Re: Re: Experience with Asus Netbook" Next in. washington. Re: external force. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. Biochemistry. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. 6 ns/day for a 100k atom system with roughly those same parameters (and. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. washington. 7b1 on NCSA Abe. You should simulate it in explicit water (or try one of the implicitRe: Protein in/out of box. I would be > happy if somebody could point me out to some scripts which help me performDCD. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). Email:. Join Facebook to connect with Gianluca Interlandi and others you may know. From: Gianluca Interlandi (gianluca_at_u. Mechanism of allosteric propagation across a β-sheet structure investigated by molecular dynamics simulations. {Gianluca Interlandi and Svava K Wetzel and Giovanni Settanni and Andreas Pl{"u}ckthun and Amedeo Caflisch}, journal={Journal of molecular biology}, year={2008},. 7b1 on NCSA Abe. 1 2 3 Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. Bioengineering. washington. 7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. You should simulate it in explicit water (or try one of the implicitOn Tue, 14 Dec 2004, Gianluca Interlandi wrote: > Dear NAMD users, > > I have two independent questions: > > 1) Are there any experiences about the scalability running NAMD on > infiniband? I have been running NAMD on myrinet and, as an example, for > a system with 51000 atoms I get a seedup of 14 on 16 CPUs (dual opteron > 1800+). Gianluca has 2 jobs listed on their profile. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. You should simulate it in explicit water (or try one of the implicit From: Gianluca Interlandi <gianluca_at_u. washington. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. washington. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the Abmer force field > parameters? > > Thanks, > Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates" Next in thread: Gianluca Interlandi: "Re: query about wrapped coordinates" Reply: Gianluca Interlandi: "Re: query about wrapped coordinates" Messages sorted by: [ attachment ] Hi, Thanks again for your useful suggestions. 7 out the door on Friday. Michel Espinoza-Fonseca: "Re: Vibrational. washington. uiuc. Search 214,979,228 papers from all fields of science. One of the two proteins has reached one of > the boundaries of the box and it has been wrapped around. edu) Date: Wed Aug 05 2009 - 13:19:25 CDT Next message: Gianluca Interlandi: "Re: SMD output : which col represents force, second or last" Previous message: David Tanner: "Re: SMD output : which col represents force, second or last" In. washington. 7 with the PLUMED patch" In reply to: Gianluca Interlandi: "Compiling NAMD 2. washington. washington. I know this can be just a detail, but it is quite tricky. See more properties from this host. Re: Yet another NAMD speed concerns. Don't take my word that this works. I empolyed PBC condition with wraping water and wraping all options on. washington. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. From: Gianluca Interlandi (gianluca_at_u. Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca Interlandi> 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallmargin errors. You simply load your trajectory > > into VMD On 7/7/2011 6:08 PM, Gianluca Interlandi wrote: > Francesco, > > Just a hint. Sunhwan On Jul 16, 2014, at 12:32 AM, Gianluca Interlandi <gianluca_at_u. > > Gianluca > > On Wed, 23 Sep 2015, John Stone. Comparative controls consisted of FocH (high affinity with and. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. > You could build a PC with the Asus p5Q Pro Motherboard, Intel Quadcore Q8200 > and two GTX 285 cards for under 900$ (plus the cost of the usual PC > components). washington. 20-23 2012)<br><br>2001 May/2002 September: Master in Tourism Management - Academy of Trade and Tourism, Trento, Italy (1900 hrs). edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. The structure was derived from the complex co-crystallized with botrocetin (PDB code 1U0N) (), because this is the only structure of the complex where 11 amino acids of the A1 N-terminal linker were resolved (other structures. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. washington. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. edu> wrote: > Roy, > > I think that you are confusing two things. What this rental offers. From: Gianluca Interlandi (gianluca_at_u. Member since 2014. Michel Espinoza-Fonseca: "Re: Vibrational. washington. 1002/prot. washington. 7b1 on NCSA Abe. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. Proteins. Research Assistant Professor (Independent Lab) e-mail: gianluca@u. washington. washington. Maybe the file was not transferred correctly to your desktop PC.