Re: [gmx-users] cross-correlations as a function of interatomic distance

On 16/03/2010 5:16 PM, shahab shariati wrote: Hi gromacs users After using g_covar for obtaining dynamic cross correlation map, how is obtained cross-correlations as a function of interatomic distance? Thank you so much for any help! I'm not even sure whether "cross-correlations as a function

[gmx-users] cross-correlations as a function of interatomic distance

Hi gromacs users After using g_covar for obtaining dynamic cross correlation map, how is obtained cross-correlations as a function of interatomic distance? Thank you so much for any help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pleas

Re: [gmx-users] g_wham error

Gard Nelson wrote: Hi all, I'm trying to analyze a series of umbrella sampling windows, but I get the following error: Program g_wham, VERSION 4.0.7 Source code file: gmx_wham.c, line: 1397 Fatal error: Found 1 pull groups in onePREP0.tpr, but 1 data columns in onePREP0.xvg (expected 6) m

[gmx-users] g_wham error

Hi all, I'm trying to analyze a series of umbrella sampling windows, but I get the following error: Program g_wham, VERSION 4.0.7 Source code file: gmx_wham.c, line: 1397 Fatal error: Found 1 pull groups in onePREP0.tpr, but 1 data columns in onePREP0.xvg (expected 6) my .mdp file is: title

[gmx-users] SiO2

Hi All, Does anyone have force field and topology of SiO2 that I can look at ? Or are they available in some crystal data bank ? Thanks in advance for the help ! - Rohit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] mix berger ff with opls

Dear Bin, I think that you are getting confused here between different publications. It was the Lindahl, E., and O. Edholm. 2000. paper that you quote below, but recall that they had no protein in that work so manipulations of fudgeQQ would have been available to them. The HEDP method is

RE: [gmx-users] test particle insertion with PME

Hi, Yes, I implemented it in git master. Berk > From: schn...@uni-heidelberg.de > Date: Mon, 15 Mar 2010 14:52:38 +0100 > To: gmx-users@gromacs.org > Subject: [gmx-users] test particle insertion with PME > > Hi all, > > has the combination of tpi (test particle insertion) and PME (particle

[gmx-users] test particle insertion with PME

Hi all, has the combination of tpi (test particle insertion) and PME (particle mesh Ewald) already been implemented into any GROMACS version? Eamnuel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.

Re: [gmx-users] gen_vel error

On 16/03/2010 12:28 AM, Carla Jamous wrote: Hi everyone, Please I made an error during my simulation: I ran my simulation in the following way for many steps: grompp -v -f md.mdp -c ax.pdb -t bx.trr -e dx.edr -o ex.tpr -p fx.top mdrun -v -s ex.tpr -o gx.trr -c hx.pdb -x ix.xtc -e md.edr -g md.log

Re: [gmx-users] gen_vel error

Carla Jamous wrote: Hi everyone, Please I made an error during my simulation: I ran my simulation in the following way for many steps: grompp -v -f md.mdp -c ax.pdb -t bx.trr -e dx.edr -o ex.tpr -p fx.top mdrun -v -s ex.tpr -o gx.trr -c hx.pdb -x ix.xtc -e md.edr -g md.log But in my em.mdp, I

[gmx-users] gen_vel error

Hi everyone, Please I made an error during my simulation: I ran my simulation in the following way for many steps: grompp -v -f md.mdp -c ax.pdb -t bx.trr -e dx.edr -o ex.tpr -p fx.top mdrun -v -s ex.tpr -o gx.trr -c hx.pdb -x ix.xtc -e md.edr -g md.log But in my em.mdp, I kept: gen_vel = yes So

Re: [gmx-users] mix berger ff with opls

On Fri, Mar 12, 2010 at 10:06:53PM -0500, chris.ne...@utoronto.ca wrote: > > Note that the "Berger" lipids were in fact developed by many people > and they have come to be named by only one of the contributors. The > reference that I use for my 1/8 scaling of the LJ 1-4 is: > > Lindahl, E., and O

Re: [gmx-users] rmsf question

On 15/03/2010 6:45 PM, Andrei Neamtu wrote: Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a

Re: [gmx-users] rmsf question

Hi Andrei, You can do it this way. But do mind that the ensemble from NMR is not meant to reflect the Boltzmann distribution. Rather it is meant to provide a number of plausible solutions given the (positive) restraints from the experiments and the force field used for the refinement. This means t

Re: [gmx-users] rmsf question

Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a frame from MD trajectory. So, in the PDB file