[gmx-users] Normal mode analysis

Dear all Gromacs user, I am trying to perform the Normal Mode Analysis protein-DNA complex in vacuum. As the complex is highly negative charge (-163)I performed the energy minimization of complex in water (to neutralize the complex). After I get the completely minimized complex, again I have do

[gmx-users] Normal Mode Analysis

Hello. I am trying to do a Normal Mode Analysis of a polymer in water. I am running my minimization right now with -DFLEXIBLE defined. How do I exclude the water from the analysis. I only want the analysis done on the polymer. Dan Sponseller PhD student, George Mason University -- Gromacs Use

[gmx-users] Normal Mode Analysis

Dear all, I wonder if there is anywhere I can know the details of mdp files used for normal mode analysis. I understand from the maunal that it needs steepest descent, conjugate gradient, l-bfgs, nm in "md" options consecutively, but I am not sure about other parameters set in these different s

[gmx-users] Normal Mode Analysis

Hello All, I am simulating two proteins in solution and would like to perform Normal Mode Analysis on trajectory snapshots. I take one particular frame in the trajectory and minimize it, followed by mdrun for normal mode analysis. However I am getting constraint errors in each of the two steps - 1

[gmx-users] Normal mode analysis

?Hello, Currently I am trying to perform a normal mode analysis on my pdb file using Gromacs 2019.3. But during energy minimalisation I can't seem te get my energy low enough. it remains around 10^01-10^00. I used the attached mdp-files. Am I doing something wrong? If so, what am I doing wr

[gmx-users] Normal Mode Analysis

Dear users, I am trying to do NMA First i did energy minimization using .mdp file with conjugate gradient method, Next i calculated hessian matrix by using integrator = nm Then i calculated the eigen vectors from 7 to 100 using g_nmeig to analyze eigen vectors i use the comm

[gmx-users] normal mode analysis

Dear gromacs users, I am interested in normal mode analysis, but i have no idea about the time needed for NMA compared with the regular MD. My friend who uses NAMD, and he told me that the NMA took much time. The reason may be that he used all-atom force field, can anyone tell me whether gro

[gmx-users] Normal mode analysis error

Dear all, I am trying to perform the Normal Mode Analysis protein in water. Here is the .mdp file I am using: integrator = nm; time step nsteps = 10 ; number of steps nstlist = 10; update pairli

Re: [gmx-users] Normal mode analysis

Hi Rahul, Did you make the vacuum minimization with a double-precision version of gromacs using the L-BFGS algorithm? From the protocol you described it seems you didn't do it.. What was the maximum force after the minimization? (check the .log file) I hope it helps, Leandro. On Sat,

Re: [gmx-users] Normal Mode Analysis

Perhaps, trjconv -- to delete all you do not need? On Wed, Oct 14, 2015 at 2:49 PM, Dan Sponseller wrote: > Hello. > > I am trying to do a Normal Mode Analysis of a polymer in water. I am > running my minimization right now with -DFLEXIBLE defined. > > How do I exclude the water from the a

[gmx-users] Normal mode analysis problem

Hi all I am running a normal mode analysis on a system with 1.05 million atoms without solvent. I performed extensive double precision energy minimization using conjugate gradient (more than 14 days using 1024 processor). and my final values are: Potential Energy = -8.54191598792831e+06 Max

Re: [gmx-users] Normal Mode Analysis

Den 2019-10-16 kl. 23:31, skrev Adip Jhaveri: Hello All, I am simulating two proteins in solution and would like to perform Normal Mode Analysis on trajectory snapshots. I take one particular frame in the trajectory and minimize it, followed by mdrun for normal mode analysis. However I am gettin

Re: [gmx-users] Normal Mode Analysis

Thank you for the response. But how will the system be affected when I remove the constraints? I am trying to get a measure of the entropy by the normal mode analysis, so will removing the constraints lead to an incorrect estimation? Regards, Adip On Thu, Oct 17, 2019 at 4:06 AM David van der Spo

Re: [gmx-users] Normal mode analysis

Yes I used double precision for everything. -Katrien From: Smith, Micholas D.<mailto:smit...@ornl.gov> Sent: woensdag 26 februari 2020 13:39 To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> Subject: Re: [gmx-users] Normal mode analysis Is your build of GROMACS

Re: [gmx-users] Normal mode analysis

for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Katrien Clerx Sent: Wednesday, February 26, 2020 6:31 AM To: gmx-us...@gromacs.org Subject: [EXTERNAL] [gmx-users] Normal mode analysis ?Hello, Currently I am trying

Re: [gmx-users] Normal mode analysis

National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Katrien Clerx Sent: Wednesday, February 26, 2020 7:52 AM To: gmx-us...@gromacs.org Subject: [EXTERNAL] Re: [gmx-users] Normal mode analysis

Re: [gmx-users] Normal mode analysis

> Sent: woensdag 26 februari 2020 14:10 To: Katrien Clerx<mailto:katrien.cl...@student.kuleuven.be>; gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> Subject: Re: [gmx-users] Normal mode analysis Hmmm How did you prepare the structure? Also, attachments are stripped from e

Re: [gmx-users] Normal mode analysis

Biophysics From: Katrien Clerx Sent: Wednesday, February 26, 2020 8:29 AM To: Smith, Micholas D. ; gmx-us...@gromacs.org Subject: [EXTERNAL] RE: [gmx-users] Normal mode analysis My structure does not contain any ions. Here are the commands that I used: gmx_d

Re: [gmx-users] Normal Mode Analysis

>From g_nmeig -h: An ensemble of structures can be generated from the eigenvectors with g_nmens. Cheers, Tsjerk On Mon, Nov 25, 2013 at 5:05 PM, Sathish Kumar wrote: > Dear users, > >I am trying to do NMA > > First i did energy minimization using .mdp file with conjugate g

Re: [gmx-users] Normal Mode Analysis

Is that ensemble of structures are related to each eigen vector or total eigen vectors. If i want to see the motion of seventh eigen vector how can i get? On Mon, Nov 25, 2013 at 9:50 PM, Tsjerk Wassenaar wrote: > From g_nmeig -h: > > An ensemble of structures can be generated from the eigenve

Re: [gmx-users] Normal Mode Analysis

Hi Sathish, Have you tried reading the g_nmens manpage or the manual? Cheers, Tsjerk On Mon, Nov 25, 2013 at 6:00 PM, Sathish Kumar wrote: > Is that ensemble of structures are related to each eigen vector or total > eigen vectors. > > If i want to see the motion of seventh eigen vector how ca

Re: [gmx-users] Normal Mode Analysis

, etc...   Stephan Watkins Gesendet: Montag, 25. November 2013 um 17:05 Uhr Von: "Sathish Kumar" An: "Discussion list for GROMACS users" Betreff: [gmx-users] Normal Mode Analysis Dear users, I am trying to do NMA First i did energy minimization using .mdp file with conjuga

Re: [gmx-users] normal mode analysis

Hi Fugui, It uses whatever you put into it. You could try Martini. But should you want to? It sounds like you should do a bit more background reading. Cheers, Tsjerk On Nov 25, 2013 10:45 PM, "xiao" wrote: Dear gromacs users, I am interested in normal mode analysis, but i have no idea about

Re: [gmx-users] Normal Mode Analysis

; *An:* "Discussion list for GROMACS users" > *Betreff:* [gmx-users] Normal Mode Analysis > Dear users, > > I am trying to do NMA > > First i did energy minimization using .mdp file with conjugate gradient > method, > > Next i calculated hessian matrix by using

Re: [gmx-users] Normal Mode Analysis

Sorry,   Your correct. Thanks for correcting me.  I dont want to send people off on tangents, and thus appologise.    Stephan   Gesendet: Dienstag, 26. November 2013 um 07:43 Uhr Von: "Tsjerk Wassenaar" An: "Discussion list for GROMACS users" Betreff: Re: [gmx-users]

Re: [gmx-users] Normal Mode Analysis

r GROMACS users" Betreff: Re: [gmx-users] Normal Mode Analysis Hi Stephen, You're confusing NMA with PCA. Cheers, Tsjerk On Tue, Nov 26, 2013 at 6:30 AM, lloyd riggs wrote: > I don't know your energy break down, if you look at frames with g_anaeig > using -first and -last to

Re: [gmx-users] Normal Mode Analysis

:43 Uhr > *Von:* "Tsjerk Wassenaar" > *An:* "Discussion list for GROMACS users" > *Betreff:* Re: [gmx-users] Normal Mode Analysis > Hi Stephen, > > You're confusing NMA with PCA. > > Cheers, > > Tsjerk > > > On Tue, Nov 26, 2013 at 6:30

[gmx-users] normal mode analysis - regd

Dear Gromacs users, I am performing normal mode analysis (NMA) for a crystal, but in the vibrational spectrum that obtained from NMA, there are no low frequency lattice modes ( i.e., no peaks in spectrum below 50 cm-1). But the spectrum that have obtained from velocity auto correl

Re: [gmx-users] Normal mode analysis error

On 3/17/15 8:16 AM, rahul dhakne wrote: Dear all, I am trying to perform the Normal Mode Analysis protein in water. Here is the .mdp file I am using: integrator = nm; time step nsteps = 10 ; number of steps nstlist

[gmx-users] Normal mode analysis after equilibration

Dear All, I am running simulations of a toxin placed in the middle of a bilayer. It is known from the experiments that the equilibrium point of the toxin is in one of the surfaces of the membrane. I run MD with v-rescale a number of time-steps big enough to get the system equilibrated with the tox

[gmx-users] Normal-mode analysis in Gromacs

Dear Users, I have encountered several questions when I try to perform NMA on a protein structure from an equilibrated MD simulation. I were basically referred to the gromacs manual ( http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis) and some threads in the mailing list. First, G

[gmx-users] normal mode analysis and system size ...

hi , I've been trying to perform a nromal mode analysis using (after a thorough energy minimization of my system) prompt> mdrun_d -v -s nm.tpr  -o nm.trr -mtx nm.mtx[...] Maximum force: 8.56366e+00 The force is probably not small enough to ensure that you are at a minimum. Be aware that negative

Re: [gmx-users] Normal mode analysis after equilibration

On 14/01/16 18:23, Mario Fernández Pendás wrote: Dear All, I am running simulations of a toxin placed in the middle of a bilayer. It is known from the experiments that the equilibrium point of the toxin is in one of the surfaces of the membrane. What is an "equilibrium point"? I run MD with v

Re: [gmx-users] Normal mode analysis after equilibration

Dear David, Thank you very much for your answer. 2016-01-14 20:20 GMT+01:00 David van der Spoel : > On 14/01/16 18:23, Mario Fernández Pendás wrote: > >> Dear All, >> >> I am running simulations of a toxin placed in the middle of a bilayer. It >> is known from the experiments that the equilibriu

Re: [gmx-users] Normal-mode analysis in Gromacs

Den 2018-03-08 kl. 00:53, skrev Kevin C Chan: Dear Users, I have encountered several questions when I try to perform NMA on a protein structure from an equilibrated MD simulation. I were basically referred to the gromacs manual ( http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis)

Re: [gmx-users] Normal-mode analysis in Gromacs

Thank you David for your reply. In fact, I have already been using the double precision version of Gromacs. I will greatly appreciate it if other questions could also be covered. Thanks, Kevin Den 2018-03-08 kl. 00:53, skrev Kevin C Chan: > >* Dear Users, *> >* I have encountered several questi

[gmx-users] Normal Mode Analysis with Gromacs 4.6

Hello Everyone， I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot but find little useful. My Gromacs was installed in a Linux cluster. Follows is my steps to do normal mode analysis: • pdb2gmx -ignh -ff < forcefield > -f 1SHS mutated.pdb -o mut.gro -p topol.top • editconf

Re: [gmx-users] Normal Mode Analysis with Gromacs 4.6

Hello Everyone， I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot but find little useful. My Gromacs was installed in a Linux cluster. Follows is my steps to do normal mode analysis: • pdb2gmx -ignh -ff < forcefield > -f -o mut.gro -p topol.top • editconf -f mut.gro

Re: [gmx-users] Normal Mode Analysis with Gromacs 4.6

Why are you using PME-switch? Without explicitly choosing a switch? Mark On Thu, Dec 12, 2013 at 6:45 PM, mcfc1301 wrote: > Hello Everyone， > > I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot > but > find little useful. > My Gromacs was installed in a Linux cluster. >

[gmx-users] normal mode analysis for high frequency vibrations

Hi all, I am trying to do vibrational analysis for some high frequency modes in peptides (using force field method), such as the N-H stretching, C=O stretching, N-H bending, etc. However, I got some unreasonable large frequencies, 6,000-250,000 wavenumbers, which are obviously not correct.

[gmx-users] Normal Mode Analysis failing with no error message

Hi all I am trying to do a Normal Mode Analysis on a protein assembly with 1.05 million atoms without solvent or ions. I ma trying to do so using Gromacs 5.0.4 double precision using 1024 processor and up to 256 GB of RAM, but it always fails. I do not get any error message from Gromacs in j

Re: [gmx-users] normal mode analysis for high frequency vibrations

can you give me more details? Is there any negative frequency you have found? On Fri, Jan 17, 2014 at 7:56 AM, Hao Ren wrote: > Hi all, > > I am trying to do vibrational analysis for some high frequency modes in > peptides (using force field method), such as the N-H stretching, C=O > stretching

[gmx-users] Normal mode analysis in solvent: Hessian of protein only

Dear All, I am trying to find the full normal mode frequency spectrum of a small protein. My system is composed of ~1900 atoms total, of which 130 are protein atoms and the rest are solvent atoms. Since the Hessian matrix is 3Nx3N, the full spectrum for my system consists of ~5700 eigenfrequencies