[gmx-users] How can I use template.c to calculate single point energy?

Dear GROMACS users: Is it possible to use template.c to calculate single point energy? I know template.c can analyze the trajectory information. Now I want to calculate a specific system, which contains several configurations generating from the quaternion rotations, these configurations are ind

[gmx-users] Gay-Berne potential in GROMACS

Dear All, Does anyone used Gay-Berne Potential in GROMACS before? Do I have to change the code to use this potential? I ask this question because: Recently I am planing to do some Coarse-grained simulation with Gay-Berne potential. Since I have some experience with GROMACS, I think it will be eas

Re: [gmx-users] Simulation of polarizable Carbon nanotubes

(Please don't CC me separately, just post to the list) On 6/24/15 7:32 PM, S.M. Golam Mortuza wrote: Dear Gromacs Users, I am trying to run a simulation using polarizable force field for carbon nanotube (CNT), which has 304 carbon atoms. As a test purpose, I am trying to simulate a system cont

Re: [gmx-users] GROMOS Force Field

On 6/24/15 3:46 PM, Isser, Ariel Y. wrote: Hi, I just started working with GROMACS (version 5.0) about a month ago, and I am trying to tweak the .itp file auto-generated by the PRODRG server for a small molecule. When I was comparing the PRODRG charges to those listed in the ffnonbonded.i

Re: [gmx-users] The pullf.xvg and pullx.xvg files

On 6/24/15 9:20 AM, Laura Tociu wrote: Dear Justin, Thanks for the reply! Yeah, I understand how the pulling works now. The forces at time t=0 are not zero, though. There are huge forces such as -270 or even -1700 kj/mol/nm acting on my pull group at time t=0. What do you believe could be the

Re: [gmx-users] Fwd: i want to use water_detetor.pl script

On 6/24/15 8:53 AM, Mahboobe Sadr wrote: I tried this script with ref atom O11 and also with N4 of DPPC, but it cleaned waters between leaflets and also waters below the bottom leaflet, what's the wrong? No idea. What was your exact command? I wrote the script years ago and used it probab

[gmx-users] Simulation of polarizable Carbon nanotubes

Dear Gromacs Users, I am trying to run a simulation using polarizable force field for carbon nanotube (CNT), which has 304 carbon atoms. As a test purpose, I am trying to simulate a system containing a pair of KCl ion in an infinite carbon nanotube. However, my ultimately goal is to simulate a s

Re: [gmx-users] Dynamic updating of nstlist in gromacs 5 screws up simulation results

... and first check that your observation of a differece is statistically significant. Two trajectories will be different, even from the same GROMACS version. Mark On Wed, Jun 24, 2015 at 10:42 PM Szilárd Páll wrote: > Hi, > > I think it is not very likely that the nstlist tuning would cause ve

Re: [gmx-users] Dynamic updating of nstlist in gromacs 5 screws up simulation results

Hi, I think it is not very likely that the nstlist tuning would cause very different results - especially not as a direct effect of the less frequent pair search. With nstlist updated rlist also gets recalculated; I've just checked and the estimates between 4.6 and 5.0 have not changed. You can s

[gmx-users] GROMOS Force Field

Hi, I just started working with GROMACS (version 5.0) about a month ago, and I am trying to tweak the .itp file auto-generated by the PRODRG server for a small molecule. When I was comparing the PRODRG charges to those listed in the ffnonbonded.itp file in the gromos43a1 directory, I noticed

[gmx-users] Dynamic updating of nstlist in gromacs 5 screws up simulation results

Hi, A colleague of mine and I have recently discovered that gromacs 4.6.4 and 5.0.4 give very different results in the simulation of a biomimetic polymer using an AMBER-based force field. She found that gromacs 5 mdrun is dynamically changing nstlist from 10 to 20 or 40 depending on the simulatio

Re: [gmx-users] constraint pull code / gromacs 5.0.4

CA> My nanoparticles (Radius = 1nm) are made of alumina and CA> the force field was CLAYFF I assume you realize that simulating metals within the GMX-like paradigm is physically incorrect. In short, your particles are not metallic, but crystalline clusters with vdw surface. That in itself, however

Re: [gmx-users] The pullf.xvg and pullx.xvg files

Dear Justin, Thanks for the reply! Yeah, I understand how the pulling works now. The forces at time t=0 are not zero, though. There are huge forces such as -270 or even -1700 kj/mol/nm acting on my pull group at time t=0. What do you believe could be the cause of that? And why is there a /nm in t

Re: [gmx-users] Fwd: i want to use water_detetor.pl script

I tried this script with ref atom O11 and also with N4 of DPPC, but it cleaned waters between leaflets and also waters below the bottom leaflet, what's the wrong? Best Regards M.Sadr On Wed, Jun 24, 2015 at 5:06 PM, A. mohammadzadeh < a.mohammadzadeh...@gmail.com> wrote: > > > On Sun, Jun 14,

Re: [gmx-users] constraint pull code / gromacs 5.0.4

Dear Alex, thank you for your email. The pulling rate, as it appears in your mdp, is actually zero. That mdp file was related to one single window, after having pulling one particle apart from the other one. we do not have enough info about the system. What are the nanoparticles made of? My

Re: [gmx-users] constraint pull code / gromacs 5.0.4

Dear Justin, thank you for your email. As you guessed, my mdp file was related to one indipendent window. What is atypical is the application of a constraint rather than a harmonic potential. The typical "umbrella" in "umbrella sampling." I have already tried to use the typical "umbrella"

Re: [gmx-users] Protein-DNA simulation LINKS error

On 6/24/15 7:41 AM, Timofey Tyugashev wrote: 24.06.2015 15:58, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: -- Message: 5 Date: Wed, 24 Jun 2015 05:58:47 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-DNA simulati

Re: [gmx-users] Protein-DNA simulation LINKS error

24.06.2015 15:58, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: -- Message: 5 Date: Wed, 24 Jun 2015 05:58:47 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-DNA simulation LINKS error Message-ID: <558a7f57.7000...@vt.

Re: [gmx-users] Swissparam itp file

On 6/24/15 7:19 AM, neha bharti wrote: Hello all I am trying to perform molecular dynamics simulation of ligand-protein complex in popc lipid with charmm36 force field. I am taking help from Justin A. Lemkul tutorial. First I perform orientation of protein ligand complex by following command:

[gmx-users] Swissparam itp file

Hello all I am trying to perform molecular dynamics simulation of ligand-protein complex in popc lipid with charmm36 force field. I am taking help from Justin A. Lemkul tutorial. First I perform orientation of protein ligand complex by following command: editconf -princ -f complex.gro -o complex

Re: [gmx-users] calculation of total no of hydrogen bond present in the system

Dear Rahman, I replied to this question yesterday. Please check the archives. Kind regards, Erik > On 24 Jun 2015, at 11:13, MOHD HOMAIDUR RAHMAN wrote: > > Dear All Gromacs users > > I am try to calculate total no of hydrogen bond present in a system. For > that I am using gromacs 5.0.2 (gmx

[gmx-users] calculation of total no of hydrogen bond present in the system

Dear All Gromacs users I am try to calculate total no of hydrogen bond present in a system. For that I am using gromacs 5.0.2 (gmx hbond ). The problem is that I am unable to specify donor and acceptor during input. I am using Amber coordinate and topology file that is converted to gromacs topolog

Re: [gmx-users] Fatal error: You selected groups with differen number of atoms.

Hi All Am just thinking if my mail was spammed. Thanks for any help. On Mon, Jun 22, 2015 at 4:58 PM, gromacs query wrote: > Hi All > > I want to align small residues based on 3 atom names only (ignoring rest > of the atoms) and confrms does not require same number of atoms: first.pdb > with 7

Re: [gmx-users] Protein-DNA simulation LINKS error

> On 24 Jun 2015, at 10:58, Justin Lemkul wrote: > > > > On 6/24/15 5:20 AM, Erik Marklund wrote: >> Hi Timofey, >> >> If I recall correctly, there is no constrainttype defined for the pair MCH3 >> CT in ffbonded.itp, which is needed for making a 4out virtual site for the >> methyl group in

Re: [gmx-users] Umbrella Sampling problem

On 6/23/15 10:19 PM, Lin wrote: Dear all, I follow the Umbrella Sampling tutorial, and have some problems: 1. pdb2gmx with -ter have warning "TYR-1 missiong H" So you have missing atoms or an incorrect terminus selection. The tutorial caps the N-terminus with an ACE group; if you haven't d

Re: [gmx-users] temperature problem

If you want to ask an unrelated question, please start a new thread rather than derailing an old one. On 6/24/15 2:02 AM, Lovika Moudgil wrote: Hi everyone I want to ask a question ... Like If I have Metal parameters i.e non-bonded parameters ...and I want to define its interactions wit

Re: [gmx-users] Protein-DNA simulation LINKS error

On 6/24/15 5:20 AM, Erik Marklund wrote: Hi Timofey, If I recall correctly, there is no constrainttype defined for the pair MCH3 CT in ffbonded.itp, which is needed for making a 4out virtual site for the methyl group in thymine. You need to work out the geometry that yields the correct mome

Re: [gmx-users] Protein-DNA simulation LINKS error

Hi Timofey, If I recall correctly, there is no constrainttype defined for the pair MCH3 CT in ffbonded.itp, which is needed for making a 4out virtual site for the methyl group in thymine. You need to work out the geometry that yields the correct moment of inertia for the methyl group and define