Re: [gmx-users] g_hbond

Dmitry Lupyan wrote: Dear GROMACS Users, I'm trying to use g_hbond (v4.0.3) to analyze a simulation which was generated with NAMD (trajectory was converted to .trr w/VMD). The g_hbond requires (i) a trajectory file, and (ii) a 'run input file' (tpr/tpa/tpb). How do i generate this tpr/tpa/tpb

Re: [gmx-users] g_hbond

Dmitry Lupyan wrote: Dear GROMACS Users, I'm trying to use g_hbond (v4.0.3) to analyze a simulation which was generated with NAMD (trajectory was converted to .trr w/VMD). The g_hbond requires (i) a trajectory file, and (ii) a 'run input file' (tpr/tpa/tpb). How do i generate this tpr/tpa/tp

[gmx-users] g_hbond

Dear GROMACS Users, I'm trying to use g_hbond (v4.0.3) to analyze a simulation which was generated with NAMD (trajectory was converted to .trr w/VMD). The g_hbond requires (i) a trajectory file, and (ii) a 'run input file' (tpr/tpa/tpb). How do i generate this tpr/tpa/tpb file? Is there any way

[gmx-users] Combining LJ and buckingham potential

Hi, I have tried to simulate a crystal in water solvent, however I found the error: ERROR 0 [file "new-topol3.top", line 19]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) So, my question: How can I use or define LJ potential (for water) and buckingham potential (for a

Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault

User reported it's problem with input file. 2009/4/15 annalisa bordogna : > Hi, > I received a similar error during an equilibration by steepest descent in > which I had posed constraints on water, leaving the protein free to move. > I suggest to control your mdp file... maybe you did the same thi

[gmx-users] glass transition temperature

Hi all, I have a molecule-model who's diffusivity data is available with me. Is there a way I can calculate glass transition temperature for this model from the Diffusivity data ? I do not want to perform glass transition temperature calculations. I know it can be calculated from WLF equati

[gmx-users] pull code absolute reference artifacts

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Re: [gmx-users] Hw to use the G_anaeig.................?

ajani haresh wrote: Hello every one, I was run at 1ns simulation. So, I have the one peptide simulation .trr file. Now I want analyses the g_anaeig. But I don’t know the command of this. Plz anyone tells me the HW the the analyse it and the how to use the various option in this file.

[gmx-users] Hw to use the G_anaeig.................?

Hello every one, I was run at 1ns simulation. So, I have the one peptide simulation .trr file. Now I want analyses the g_anaeig. But I don’t know the command of this. Plz anyone tells me the HW the the analyse it and the how to use the various option in this file. Plz help m

Re: [gmx-users] Temperature in Brownian Dynamics simulation

On Fri, Apr 17, 2009 at 5:32 AM, Mark Abraham wrote: > Suman Chakrabarty wrote: >> >> Hi, >> >> it was pointed out before that for Brownian Dynamics simulation, the >> temperature calculated by g_energy does not match with the ref_t in >> parameter file and it is almost double: >> http://www.groma

RE: [gmx-users] pull code absolute reference artifacts

Hi, I have no clue why you would want to fix the peptide in the middle of the box. But what you want seems to be more like com removal for the peptide only with the comm options. The pull code will do approximately what you want, but with pressure coupling there is the problem that your peptide w

[gmx-users] testing gromacs installation gmx-4.0.4; failures; success?

Dear users, We have installed gmx 4.0.4 ( single precision, on cent os 4.3 ( 32 bit ) on quad core dual xeon machine ( clock 2 GHz ) Installation directions as given on the site followed. And the tests are run using the perl script provided plus test files/folders. We find many failures ( s