Re: [gmx-users] g_tcaf use issue

On 11/11/15 03:16, Jones de Andrade wrote: > Hello. > > We are using gromacs in order to explore how well/not so well different > methods to calculate dynamical properties of liquids perform. > > At this moment, we are using g_tcaf (already seen g_energy -visc results) > to evaluate how it would

[gmx-users] Definition in martini CG force field

Dear Gromacs users, May I ask you to help me, Please? 1- I want to run the system with surfactant named Cocamide MEA in martini CG force field. I defined the beads as is follows: C-C-C-C . C1 C-C-C . C2 C-C-C . C2 O " C-C-NH . P5 C-C-OH . P2 Are the

Re: [gmx-users] How to restrain the center of gravity

Hi, On Tue, Nov 10, 2015 at 11:03 AM Hirayama, Kazunori < kazunori.hiray...@astellas.com> wrote: > Hello, this is the first post for me. My apology for any rudeness. > > My molecule of interest is a protein of about 12kD. > When I elevated temperature from 400K to 500K with .mdp file according

Re: [gmx-users] Getting a crystal topology file from pdb2gmx

Dear Justin, Thank you for your prompt reply Justin. I think that is what I was looking for but did not know such command it existed! I have tried your suggestion however another problem occurs : Opening force field file

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 45

> Is the information in the link still valid? The page is dated 09.01.07, > almost nine years ago, and refers to GROMACS 3.3. Much water has gone > under the bridge since then. Have you tried? > On choice of division and methods: I'm trying to think hard about it and > consult people

Re: [gmx-users] Getting a crystal topology file from pdb2gmx

Quick clarifying question: What force-field are you trying to use? -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From:

Re: [gmx-users] Getting a crystal topology file from pdb2gmx

On 11/11/15 11:05 AM, Ben Tam wrote: Hi Justin, I am using Gaussian with basis set 6-31G* and LanL2DZ to calculate the charges of the structure and using UFF for the lennard jones. When I answered CHARMM27, I am assuming the question was what is the option that was given when I typed 'gmx

[gmx-users] Getting a crystal topology file from pdb2gmx

Dear Gromacs users and Developer, I am trying to run a simulation for a metal organic frameworks (MOFs), it is a crystallise periodic structure. The original file is in .cif format, however using material studio I converted it to .pdb file. Now I am stuck on converting .pdb file to a topology

Re: [gmx-users] Getting a crystal topology file from pdb2gmx

Hi Justin, I am using Gaussian with basis set 6-31G* and LanL2DZ to calculate the charges of the structure and using UFF for the lennard jones. When I answered CHARMM27, I am assuming the question was what is the option that was given when I typed 'gmx pdb2gmx'. In all honesty, I have no

Re: [gmx-users] energy autocorrelation function: bug?

Dear Mario This is also a solution. Thank you for reminding. If I did not miss any input option, the reported thing is a bug of g_energy. The feature definitely worked before, up to versions around 4.0). Cordially, Vitaly On Wed, Nov 11, 2015 at 11:41 AM, Mario Fernández Pendás <

Re: [gmx-users] Getting a crystal topology file from pdb2gmx

On 11/11/15 10:37 AM, Ben Tam wrote: Hi Micholas, I am using CHARMM27. And, out of curiosity, what is the source of your Zr parameters? -Justin Ben From: smit...@ornl.gov To: gmx-us...@gromacs.org Date: Wed, 11 Nov 2015 15:26:30 + Subject: Re: [gmx-users] Getting a crystal topology

Re: [gmx-users] Getting a crystal topology file from pdb2gmx

Hi Micholas, I am using CHARMM27. Ben > From: smit...@ornl.gov > To: gmx-us...@gromacs.org > Date: Wed, 11 Nov 2015 15:26:30 + > Subject: Re: [gmx-users] Getting a crystal topology file from pdb2gmx > > Quick clarifying question: > > What force-field are you trying to use? > > -Micholas >

Re: [gmx-users] 2. QM/MM (Timofey Tyugashev)

Thank you for reply. Is the information in the link still valid? The page is dated 09.01.07, almost nine years ago, and refers to GROMACS 3.3. Much water has gone under the bridge since then. On choice of division and methods: I'm trying to think hard about it and consult people experienced

[gmx-users] energy autocorrelation function

I compute the energy ACF by using g_energy_mpi -fluc -corr However, no ACF is present in the output. Only energy.xvg is created with one column of data, which are obviously not ACF. The version is 5.0.4. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Query regarding water not settled

Hi, The standard advice for this kind of problem can be found here http://www.gromacs.org/Documentation/Terminology/Blowing_Up. In your case, you should start by asking what is the expected behaviour for your model physics, and can you reproduce those properties, before launching your own

Re: [gmx-users] Definition in martini CG force field

Hi Sara, first off, you're probably better off asking these Martini-specific questions on the Martini forum (cgmartini.nl) Secondly, some answers are inline On 11/11/15 10:57, mohammad agha wrote: > Dear Gromacs users, > May I ask you to help me, Please? > 1- I want to run the system with

Re: [gmx-users] g_tcaf use issue

Hi Peter. Sorry for the delay in answering you. Long day. ;) On Wed, Nov 11, 2015 at 5:32 AM, Peter Kroon wrote: > On 11/11/15 03:16, Jones de Andrade wrote: > > Hello. > > > > We are using gromacs in order to explore how well/not so well different > > methods to calculate

[gmx-users] Velocities with constraints

Dear Gromacs users, I am using the rigid water model TIP3P and running some dynamics. I need very accurate velocities from the output trajectory. When I do frequency decomposition of these velocities, I see that there is a non-negligible vibrational component to them, that is, the atomic

Re: [gmx-users] Velocities with constraints

I'm realizing now that the equations I'm using assume rotation about an axis that goes through the center of mass, which needs not be the case during the dynamics. This is probably the origin of the problem. Regards, Miguel -- Dr. Miguel Caro Postdoctoral researcher Department of Electrical

Re: [gmx-users] Velocities with constraints

Hi, Sounds right. Otherwise, the algorithm involved is SETTLE or RATTLE, which has an analytic solution, not LINCS. Mark On Wed, Nov 11, 2015 at 10:31 PM Caro Miguel wrote: > I'm realizing now that the equations I'm using assume rotation about an > axis that goes through

[gmx-users] problem with equilibration of DLiPC membrane

Dear all, I'm a new Gromacs user and I'm trying to build a lipid membrane with 450 DLiPC (18:2) by using 43A1-S3 forcefield. For membrane building, first I put a single DLiPC molecule in small box, then replicated it in x-y by genconf -nbox to get 450 lipid