Re: [gmx-users] temperature shooting up

Dear Mark,Thanks for your help. Actually I did separate runs for flexible and rigid models, and didn't use the equilibrated flexible structure to start with rigid model calculations. But the starting configurations are the same. So do you mean I need to reduce the T-coupling time? If the initial wa

Re: [gmx-users] Understanding the output of g_rmsf

Hi Keith, Reference frame and reference structure are references to the same reference. It is the structure supplied with -s, and possibly a subset of the atoms in there, specified by an index group. The RMSF is indeed the standard deviation of the atomic displacement. That is an atom or residue

[gmx-users] question about energy fluctuation

Hi all,After running a MD of a system with about 17000 atoms, I calculated the potential and the total-energy:*Last frame read 1557952 time 1557.952Statistics over 1557953 steps [ 0. thru 1557.9520 ps ], 2 data

Re: [gmx-users] Strange problem with simple FEP (bug?)

Thanks, but that's indeed not the problem. I'm just doing a PR-run in state A. State B is not of interest in that case. Somehow GROMACS mixes things up internally, I guess. The bugzilla-entry has been placed. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theor

[gmx-users] calculating energy for more than 256 index groups

Hi, i want to calculate an interaction energy matrix for more than 256 energy groups. First grompp only accept 255 groups so i changed in readir.c #define MAXPTR 510 #define NOGID 511 (from 254 and 255) After that grompp writes out an tpr file and mdrun works without problems, but than in

[gmx-users] Creation of an index file with seperate lipid leaflets

Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perhaps something consider

Re: [gmx-users] Creation of an index file with seperate lipid leaflets

On Wed, 8 Nov 2006, Alan Dodd wrote: > Has anyone already created a way to generate an index > file with the atoms from the two leaflets of a bilayer > listed seperately? I can't believe it hasn't already > been done, but can't find a direct description of a > solution. I'm attempting a modificat

Re: [gmx-users] Creation of an index file with seperate lipid leaflets

Wouldn't shuffle/sort undo all the good work? I did wonder if I should have labelled the lipids in different leaflets as different molecule types, or different chains, but it's a bit late now... --- Jay Mashl <[EMAIL PROTECTED]> wrote: > On Wed, 8 Nov 2006, Alan Dodd wrote: > > Has anyone alread

[gmx-users] NPH simulation, constant enthalpy?

Dear Gromacs users, I have been trying to run an NPH (constant pressure and enthalpy) simulation of a LJ fluid (as a first test) with GROMACS. From what I understand (from the GROMACS manual and references therein), one can do that by considering a Parrinello-Rahman pressure coupling (and no ther

[gmx-users] pdb2gmx and protein DNA complexes

Hi I am trying to simulate a protein DNA complex but I am stuck at the pdb2gmx stage as it gets stuck when it encounters a nucleotide.Program pdb2gmx, VERSION 3.3Source code file: resall.c, line: 438 Fatal error:Residue 'C' not found in residue topology databaseThe pdb segment is as follows:ATOM  

Re: [gmx-users] Creation of an index file with seperate lipid leaflets

Alan Dodd a écrit : Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perh

Re: [gmx-users] Creation of an index file with seperate lipid leaflets

On Wed, Nov 08, 2006 at 10:09:28AM -0600, Jay Mashl wrote: > On Wed, 8 Nov 2006, Alan Dodd wrote: > > Has anyone already created a way to generate an index > > file with the atoms from the two leaflets of a bilayer > > listed seperately? I can't believe it hasn't already > > been done, but can't f

Re: [gmx-users] Creation of an index file with seperate lipid leaflets

Wasted work would be bad ;) Rather than headgroup orientation, maybe try looking at atom distributions along the bilayer normal direction. Neutron scattering experiments show that for atom groups far from the bilayer midplane, the corresponding z-coordinates form two distinct distributions.

Re: [gmx-users] pdb2gmx and protein DNA complexes

Yes, very recently actually. What forcefield are you using? If you're using the AMBERXX-port, you might want to have a look at http://folding.stanford.edu/ffamber/. Regardless of your ff, make sure that the atoms in your pdb match the ones in ff[your_forcefield].rtp. Oh, and read the manual.

Re: [gmx-users] pdb2gmx and protein DNA complexes

...and not just the atoms. Make sure that the residue names are the correct ones for your forcefield. Apparently, the forcefield you're using does not have a 'C'-residue.   /Erik - Original Message - From: Erik Marklund To: Discussion list for GROMACS users Sent: W

[gmx-users] How to generate GRO and TOP file for high-number-atom polymer?

Hi,    Genearlly I generate GRO and TOP file for polymer using PRODRG. But PRODRG does not work when the atom number of the polymer exceeds 300. So can anyone recommend other software and method? Thanks. Yours Sincerely

[gmx-users] What if the atom number exceed 99999 for Gromacs file?

Hi, I built up a box of polymer with box size 20x20x20 and then solvate the box with water using Genbox. Thus the total atom number exceeds 9 and I found that the atom number starts from zero when it exceeds 9. Does it matter for the ongoing command "grompp" and "mdrun"? Thanks.   

Re: [gmx-users] What if the atom number exceed 99999 for Gromacs file?

I believe, It does not matter. On 11/8/06, WU Yanbin <[EMAIL PROTECTED]> wrote: Hi, I built up a box of polymer with box size 20x20x20 and then solvate the box with water using Genbox. Thus the total atom number exceeds 9 and I found that the atom number starts from zero when it exceeds 99

Re: [gmx-users] temperature shooting up

Cherry Y. Yates wrote: Dear Mark, Thanks for your help. Actually I did separate runs for flexible and rigid models, and didn't use the equilibrated flexible structure to start with rigid model calculations. But the starting configurations are the same. Oh OK - but the same kind of problem

Re: [gmx-users] question about energy fluctuation

Qiao Baofu wrote: Hi all, After running a MD of a system with about 17000 atoms, I calculated the potential and the total-energy: * Last frame read 1557952 time 1557.952 Statistics over 1557953 steps [ 0.

Re: [gmx-users] invalid order of directive moleule type

Thanks for the valueable suggessions, but sir i am actually want to use this program for small molecules. I have taken single FAD molecule as u suggested modified the atom type as described in ffgmx.rtp, program results top and gro files using pdb2gmx, but while running grompp i am getting th

Re: [gmx-users] How to generate GRO and TOP file for high-number-atom polymer?

Hi Wu Yanbin, Define the polymer building block and add it to the residue database file of your liking (ff*.rtp). Then you can use pdb2gmx to build the topology of your polymer chain. Do take some time to understand the .rtp file/entry format. Best, Tsjerk On 11/8/06, WU Yanbin <[EMAIL PROTECT

Re: [gmx-users] What if the atom number exceed 99999 for Gromacs file?

Hi, Atom numbers in structure files are not used. Atoms read from a file are given fresh numbers from 1 through N, where N is the total number of atoms. Best, Tsjerk On 11/9/06, Viswanadham Sridhara <[EMAIL PROTECTED]> wrote: I believe, It does not matter. On 11/8/06, WU Yanbin <[EMAIL PROT

Re: [gmx-users] question about energy fluctuation

Mark Abraham wrote: Qiao Baofu wrote: Hi all, After running a MD of a system with about 17000 atoms, I calculated the potential and the total-energy: * Last frame read 1557952 time 1557.952 Statistics ove

Re: [gmx-users] NPH simulation, constant enthalpy?

Adrien Leygue wrote: Dear Gromacs users, I have been trying to run an NPH (constant pressure and enthalpy) simulation of a LJ fluid (as a first test) with GROMACS. From what I understand (from the GROMACS manual and references therein), one can do that by considering a Parrinello-Rahman pressure

Re: [gmx-users] question about energy fluctuation

Thanks. but the g_energy -nmol can only give the Bond,Angle data divided by the nmol, for the Proper-Dih. LJ, Coulomb, Potential, Total-Energy, g_energy -nmol 981 gives the same result as without -nmol 981, in which 981 is the number of molecules.I am using Gromacs 3.3.1. You can divide by the num