[gmx-users] problem in gmx-users list archive?

Dear administrators of gmx-users list, I would like to report a problem in the gmx-users list archive (or at least in its visualization in the Web site). Starting from 2011, when I search in the archive on the Gromacs web site, I can see that multiple copies of identical messages are reported in th

Re: [gmx-users] problem in gmx-users list archive?

On 19/05/2011 6:25 PM, Anna Marabotti wrote: Dear administrators of gmx-users list, I would like to report a problem in the gmx-users list archive (or at least in its visualization in the Web site). Starting from 2011, when I search in the archive on the Gromacs web site, I can see that multip

[gmx-users] simulation of a peptide anchored to a support

Dear gmx-users, I would like to simulate the conformational behaviour of a peptide covalently anchored to a rigid support with its N- and C-ter. I'm not interested in simulating the support, so I wonder if there is a way to simulate the peptide with its N- and C-ter fixed. Could freezegrps work for

Re: [gmx-users] simulation of a peptide anchored to a support

On 19/05/2011 7:09 PM, Anna Marabotti wrote: Dear gmx-users, I would like to simulate the conformational behaviour of a peptide covalently anchored to a rigid support with its N- and C-ter. I'm not interested in simulating the support, so I wonder if there is a way to simulate the peptide with

[gmx-users] g_msd query

Hi ALL, I am trying to calculate the lateral diffusion coefficient of a protein in a bilayer (CG simulation using MARTINI FF). The simulation length is 5 micro-seconds. I wanted to know based on what should i set the values of -beginfit and -endfit and also the value for -trestart. Is it necessary

Re: [gmx-users] g_msd query

Anirban Ghosh skrev 2011-05-19 11.58: Hi ALL, I am trying to calculate the lateral diffusion coefficient of a protein in a bilayer (CG simulation using MARTINI FF). The simulation length is 5 micro-seconds. I wanted to know based on what should i set the values of -beginfit and -endfit and al

R: Re: [gmx-users] simulation of a peptide anchored to a support

uctuation of the peptide into > the solvent? Not sure what you mean. > Finally, do I have to add special constraints/restraints to my molecule? Depends on the strategy. Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/

Re: [gmx-users] reg centre of mass in SMD

vidhya sankar wrote: Thank you Dr Justinj, To do SMD should i create centre of mass of my reference (protein) and pull group (ligand)? if i need to create , which tool of gromacs generate to be used .? How to include this center of mass in SMD .mdp files N

[gmx-users] average trajectory

Dear gromacs users, 1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns). I want to make a distance matrix (*g_mdmat*) for the average trajectory of these 3 runnings. *g_mdmat* gives an average matrix for one trajectory, but I want to get it for the average trajectory. I tried t

[gmx-users] About -pbc option of trjconv

Hi ALL, I have a long simulation trajectory of 3 micro-seconds of multiple protein monomers in a lipid bilayer. Which -pbc option should be used with trjconv to process the trajectory before carrying out any analysis? I am using -pbc nojump, is it correct? Or should I use -pbc whole? Thanks a lot

Re: [gmx-users] About -pbc option of trjconv

Anirban Ghosh wrote: Hi ALL, I have a long simulation trajectory of 3 micro-seconds of multiple protein monomers in a lipid bilayer. Which -pbc option should be used with trjconv to process the trajectory before carrying out any analysis? I am using -pbc nojump, is it correct? Or should I u

Re: [gmx-users] average trajectory

Yulian Gavrilov wrote: Dear gromacs users, 1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns). I want to make a distance matrix (*g_mdmat*) for the average trajectory of these 3 runnings. *g_mdmat* gives an average matrix for one trajectory, but I want to get it for

Re: [gmx-users] average trajectory

Justin A. Lemkul skrev 2011-05-19 14.30: Yulian Gavrilov wrote: Dear gromacs users, 1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns). I want to make a distance matrix (*g_mdmat*) for the average trajectory of these 3 runnings. *g_mdmat* gives an average matrix for

[gmx-users] Fwd: energy groups in tabulated potentials

Please do not send unsolicited email requesting private help. I am forwarding this to the appropriate forum. On point, I think the examples and explanations given in various manual sections deal with your case. Mark Original Message Subject:energy groups in tabulate

Re: [gmx-users] average trajectory

Hey, If you can sum them, the only thing needed afterwards is updating the color labels. Like per awk (dividing by two): awk -F\" '/#/{$4=$4/2}1' file.xpm Cheers, Tsjerk On Thu, May 19, 2011 at 2:43 PM, Erik Marklund wrote: > Justin A. Lemkul skrev 2011-05-19 14.30: >> >> >> Yulian Gavrilov

Re: R: Re: [gmx-users] simulation of a peptide anchored to a support

tide into the solvent? Not sure what you mean. Finally, do I have to add special constraints/restraints to my molecule? Depends on the strategy. Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2011

[gmx-users] Manually aborting a simulation

Hi, I have started a lengthy equilibration run, and I just realized that I have one of my parameters set incorrectly in my mdp file. Is there any way that I can manually abort the run? I am using Gromacs 4.5.4 with parallel simulation with MPI and the command: mpirun -machinefile cp -np 8 md

Re: [gmx-users] Manually aborting a simulation

Andrew DeYoung wrote: Hi, I have started a lengthy equilibration run, and I just realized that I have one of my parameters set incorrectly in my mdp file. Is there any way that I can manually abort the run? I am using Gromacs 4.5.4 with parallel simulation with MPI and the command: mpiru

[gmx-users] water dimer is gas phase

Hello, I am trying a simulation for water dimer in vaccum (gas phase). Here I run the simulation with following steps This is the .pdb file before energy minimization TITLE S C A M O R G REMARKTHIS IS A SIMULATION BOX CRYST13.0003.0003.000 90.00 90.00 90.00 P 1

[gmx-users] Re: water dimer is gas phase

> the equlibration file I used > > title               =  cpeptid position restraining > cpp                 =  /usr/bin/cpp > constraints         =  none > integrator          =  md > dt                  =  0.001    ; ps ! > nsteps              =  100      ; total 1.0 ps. > nstcomm            

Re: [gmx-users] Re: water dimer is gas phase

if I set pbc=xyz in energy minimization mdp file then I get following error ERROR: can only have neighborlist cut-off zero (=infinite) with coulombtype = Cut-off or coulombtype = User and simple neighborsearch without periodic boundary conditions (pbc = no) and rcoulomb and rvdw set to zero ERRO

Re: [gmx-users] Re: water dimer is gas phase

Vitaly Chaban wrote: the equlibration file I used title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001; ps ! nsteps = 100 ; total 1.0 ps. nstcomm

Re: [gmx-users] Re: water dimer is gas phase

> > For vacuum systems, "pbc = no" in conjunction with zero cutoffs is correct > to obtain a gas-phase system. For reasonably large box, this is the same heck. Nilesh: visualize your system, using VMD or ngmx. The behavior of your molecular cluster during the first ps will provide an answer. Are

Re: [gmx-users] Re: water dimer is gas phase

Very good. Have you take a moment to define the box in the GRO file? -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 On Thu, May 19, 2011 at 4:05 PM, Nilesh Dhumal wrote: > if I set pbc=xyz in energy minimization mdp file  then I get

Re: [gmx-users] Re: water dimer is gas phase

Vitaly Chaban wrote: For vacuum systems, "pbc = no" in conjunction with zero cutoffs is correct to obtain a gas-phase system. For reasonably large box, this is the same heck. Setting a box size and using "pbc = xyz" precludes the use of infinite cutoffs, which should be the most rigorous

[gmx-users] issue with newest version of martini model

I am getting ab error with the newest version of the martini model in which seq2itp, atom2cg generate structures with a topology mismatch if there are any alanines in the structure 9. mutating out the alanines seems to resolve the problem? are there any bug fixes out there? thanks jeremy -- gmx-

Re: [gmx-users] issue with newest version of martini model

jeremy adler wrote: I am getting ab error with the newest version of the martini model in which seq2itp, atom2cg generate structures with a topology mismatch if there are any alanines in the structure 9. mutating out the alanines seems to resolve the problem? are there any bug fixes out there

[gmx-users] X-ray Structures

Hi, I have a question about using X-ray PDB files for simulations: 1. Is there any rule of thumb on how good a resolution is required for simulations? I know it has nothing to do with GROMACS. Thanks for your insight. Simon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromac

Re: [gmx-users] Manually aborting a simulation

On 20/05/2011 3:45 AM, Justin A. Lemkul wrote: Andrew DeYoung wrote: Hi, I have started a lengthy equilibration run, and I just realized that I have one of my parameters set incorrectly in my mdp file. Is there any way that I can manually abort the run? I am using Gromacs 4.5.4 with parall

Re: [gmx-users] X-ray Structures

On 20/05/2011 7:38 AM, simon sham wrote: Hi, I have a question about using X-ray PDB files for simulations: 1. Is there any rule of thumb on how good a resolution is required for simulations? Not really. The lower the resolution, the more likely that the initial conditions for the simulatio

[gmx-users] problem during energy minimization

Dear Gmx users, I am trying to do minimization of my system .i have no problem wehen i grompp it but when i do the mdrun its giving me some segmentation error.I had attached the output of grompp and mdrun below.Any suggestions please.Thanks in advance *OUTPUT OF GROMPP*

Re: [gmx-users] problem during energy minimization

sreelakshmi ramesh wrote: Dear Gmx users, I am trying to do minimization of my system .i have no problem wehen i grompp it but when i do the mdrun its giving me some segmentation error.I had attached the output of grompp and mdrun below.Any suggestions please.Tha

Re: [gmx-users] problem during energy minimization

hai, to check if my table is correct i just copied the 6-9 table for /share/top to local directory ( to check if the prob is same with any other potential) and grompped it and when i did the mdrun i am still getting the same error.Any suggestions. On Fri, May 20, 2011 at 6:29 AM, Jus

[gmx-users] problem during energy minimization

1. you're not doing energy minimization as your title suggests, please use a better title: integrator = md 2. generally, when you have a problem it is useful to try to simplify the system (e.g. get rid of those tables) and try to reproduce the problem with the simplest system possible be

[gmx-users] segmentation fault.

dear gmx-users, During equilibriation i get the following error.Any suggestions please. *grompp* WARNING 1 [file npt.mdp]: The sum of the two largest charge group radii (2.369582) is larger than rlist (1.00) This run will generate roughly 73 Mb of data There wa