Re: [gmx-users] non-standard residues in pdb2gmx

Hi, What might be even easier is to create an .itp file for myristic acid, so you can #include myristic.itp in any topology that needs it.  That way you don't have to mess with .rtp files, or run pdb2gmx for every system that contains myristic acid. But this doesn't help when it has to be

Re: [gmx-users] Shell dynamics with vdW terms.

On Tuesday 09 June 2009 18:27:16 Berk Hess wrote: From: raf...@us.es To: gmx-users@gromacs.org Subject: Re: [gmx-users] Shell dynamics with vdW terms. Date: Tue, 9 Jun 2009 16:29:39 +0200 On Tuesday 09 June 2009 10:02:47 Berk Hess wrote: Hi, The equation you refer to is only

Re: [gmx-users] units of eigenvalues of mass-weighted covariance matrix

Hi, Well, as has been pointed out before nm\S2\N stands for nm superscript 2 normal. That is correct for non mass-weigthed covariance analysis. It's just fluctuation. Why would it be kg/m2 (kg/nm2) for mass weighted? Look at the equations in the manual. It's sqrt(mass)*sqrt(mass)*nm*nm, which

[gmx-users] x2top_d running for too long

Hi All, I am trying to generate the topology file for some molecule using x2top_d. I have fired the command as: *x2top_d -f Bromo-WR99210.pdb -o Bromo-WR99210.top -r Bromo-WR99210.rtp *This is executing from last 16 hours, I dont know whether it takes this much time or is there any problem

Re: [gmx-users] x2top_d running for too long

vivek sharma wrote: Hi All, I am trying to generate the topology file for some molecule using x2top_d. I have fired the command as: */x2top_d -f Bromo-WR99210.pdb -o Bromo-WR99210.top -r Bromo-WR99210.rtp /*This is executing from last 16 hours, I dont know whether it takes this much time

RE: [gmx-users] Shell dynamics with vdW terms.

From: raf...@us.es To: gmx-users@gromacs.org Subject: Re: [gmx-users] Shell dynamics with vdW terms. Date: Wed, 10 Jun 2009 08:42:26 +0200 On Tuesday 09 June 2009 18:27:16 Berk Hess wrote: From: raf...@us.es To: gmx-users@gromacs.org Subject: Re: [gmx-users] Shell dynamics with

[gmx-users] Re: trouble for old/new GROMACS site

Dear Justin, thank you for the link you provided me, using it I'm able to find the gmx-user archive. However, when I'm clicking directly on the link to the old GROMACS site provided in the new home page: http://oldwww.gromacs.org the old home page opens with a series of warnings such as:

Re: [gmx-users] Re: trouble for old/new GROMACS site

Anna Marabotti wrote: Dear Justin, thank you for the link you provided me, using it I'm able to find the gmx-user archive. However, when I'm clicking directly on the link to the old GROMACS site provided in the new home page: http://oldwww.gromacs.org the old home page opens with a series of

Re: [gmx-users] x2top_d running for too long

Hi Mark, Thanks for your reply. But I didn't got what does it mean? 2009/6/10 Mark Abraham mark.abra...@anu.edu.au vivek sharma wrote: Hi All, I am trying to generate the topology file for some molecule using x2top_d. I have fired the command as: */x2top_d -f Bromo-WR99210.pdb -o

Re: [gmx-users] x2top_d running for too long

vivek sharma wrote: Hi Mark, Thanks for your reply. But I didn't got what does it mean? It's a bug. Please try one of the other programs from the download section on the website, e.g. topolbuild. 2009/6/10 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au vivek

[gmx-users] problem in running grompp

hi, i am simulating a membrane protein inside dppc bilayer and in this regard i am following justin's tutorial. but i ma facing a problem in running grompp...whenever i run it is giving error Program grompp, VERSION 4.0.5 Source code file: grompp.c, line: 362 Fatal error: number of

[gmx-users] Re: problem in running grompp

Samik Bhattacharya wrote: hi, i am simulating a membrane protein inside dppc bilayer and in this regard i am following justin's tutorial. but i ma facing a problem in running grompp...whenever i run it is giving error Program grompp, VERSION 4.0.5 Source code file: grompp.c, line: 362

[gmx-users] vdwradii.dat - where do the values come from?

Hi there GMX users, Does anyone know where do the van der waals radii values that are in the vdwradii.dat come from? I've searched the archives and David said once that he didn't recall where they were token from. If there is no information whatsoever of where do they come from and since it would

[gmx-users] problem fitting trajectory

Hello, I have done a simulation using Gromacs 4 (4.0.2) and I would like to have a trajectory were the protein is fitted to the first structure (to mantain the exact orientation). When I have tried echo 1 1 0 | trjconv -f production_1_3.xtc -s production1.tpr -center -fit rot+trans -pbc mol

Re: [gmx-users] problem fitting trajectory

I have found that the combination of -pbc mol -ur compact always looks pretty :) So in addition to -fit and perhaps -center, try those two options together. -Justin Rebeca García Fandiño wrote: Hello, I have done a simulation using Gromacs 4 (4.0.2) and I would like to have a trajectory

[gmx-users] Small molecule-protein complexes MD simulations

This is of course the question which was discussed many times, but I just want to ask about updates for it. Is there any port for GAFF force field now? Is it possible to prepare small molecule ligands for GROMACs MD with Amber force fields without Amber version installed? Best regards, Andrew

Re: [gmx-users] Small molecule-protein complexes MD simulations

Andrew Voronkov wrote: This is of course the question which was discussed many times, but I just want to ask about updates for it. Is there any port for GAFF force field now? Is it possible to prepare small molecule ligands for GROMACs MD with Amber force fields without Amber version

[gmx-users] g_energy returns the instantaneous data or the average data?

Hi I want to calculate the pressure and the energy for the system. my .mdp file is as follows; writing out the energy and coordinates per 1000 steps. nstenergy = 1000 ; Writing out energy information every step nstxtcout = 1000 ; Writing coordinates every step After entering g_energy

Re: [gmx-users] g_energy returns the instantaneous data or the average data?

Chih-Ying Lin wrote: Hi I want to calculate the pressure and the energy for the system. my .mdp file is as follows; writing out the energy and coordinates per 1000 steps. nstenergy = 1000 ; Writing out energy information every step nstxtcout = 1000 ; Writing coordinates every step

Re: [gmx-users] problem fitting trajectory

Hi, This is a recurrent issue. I have figured a bash script that had worked for every system which I had tested (i.e. protein, protein-ligand, protein-DNA, protein-protein), but this is not a warranty. It centers the protein on the box, and at the same time puts waters inside the box ; however the

[gmx-users] problem regarding removal of water from final simulation system.

Dear all I have done successfully simulation of membrane protein , but after that to visualise my final model clearly I have to remove water molecules from my system (protein+lipid+water). But I have no Idea about the which command I should use to do this even it doesn't mentioned in justin,s

RE: [gmx-users] problem regarding removal of water from final simulation system.

Two ways: 1 - turn them off with the visualisation software you are using, only display the protein and lipid 2 - use editconf and the appropriate index groups Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash

Re: [gmx-users] problem regarding removal of water from final simulation system.

nitu sharma wrote: Dear all I have done successfully simulation of membrane protein , but after that to visualise my final model clearly I have to remove water molecules from my system (protein+lipid+water). But I have no Idea about the which command I should use to do this even it