[gmx-users] NVT equilibration of ethanol in OPLSAA ff

Dear All, I downloaded ethanol.pdb file from prodrg server (all-atom). I used ethanol.itp file that was in oplsaa.ff directory of gromacs to create topology file for ethanol. I used genconf_d command to generate solvent box of 512 molecules (as of Bevan's gromacs tutorial) and then I

[gmx-users] angke definition

Hi, i need your help again! this time in the selection of analyzing tools and methods... I've found a water molecule near one of the ligand atoms. It's stabile enough and the distance is about 3.3 A. But I want to make some measurments, exactly angle degree identification. I want to calculate the

Re: [gmx-users] NVT equilibration of ethanol in OPLSAA ff

On 5/10/2011 6:36 PM, Ravi Kumar Venkatraman wrote: Dear All, I downloaded ethanol.pdb file from prodrg server (all-atom). I used ethanol.itp file that was in oplsaa.ff directory of gromacs to create topology file for ethanol. I used genconf_d command to generate solvent box of

Re: [gmx-users] angke definition

Hey :) Would g_sgangle be capable of what you want? Otherwise, your best bet seems to be writing the atoms involved to an easily readable format (.gro/.pdb) and do the math in Python. I can send you a backbone Python script for reading .gro/.pdb trajectories if you want. Cheers, Tsjerk On

Re: [gmx-users] angke definition

On 5/10/2011 7:28 PM, Tsjerk Wassenaar wrote: Hey :) Would g_sgangle be capable of what you want? Otherwise, your best bet seems to be writing the atoms involved to an easily readable format (.gro/.pdb) and do the math in Python. I can send you a backbone Python script for reading .gro/.pdb

[gmx-users] NVT equilibration.

Dear All, My commands where, genconf_d -f ethanol.gro -o ethanol512.gro -nbox 8 8 8 editconf_d -f eth512.gro -density 785.22 -o den.gro I saw the den.gro by using VMD. I saw only as points but not the molecules. EM: grompp_d -f em.mdp -c den.gro -p ethanol.top -o em.tpr

[gmx-users] protein_model_refinement

Dear All I am trying to refine a protein model which is a homodimer with each chain having 609 residues.I tried minimizing in Chimera and then checking models with procheck.Infact model quality deteriorated as far as Ramachandran plot is concerned. Will doing MD simulation help me in Gromacs. It

[gmx-users] RE:Data Analysis

Dear All, I woundered if anyone has scripts/tools or suggestions for analyzing energy changes from extracted run data. Mostly I end up with 20 spread sheet columns for a large system with 2x2 domain proteins, a peptide of 10-20 amino acids and soome small molecules. I've been playing with

[gmx-users] dihedral restraints documentation

Just a note concerning dihedral restraints documentation -- the function and default behavior of dihre-fc needs to be documented somewhere in the manual. I just spent a couple hours (and my student a couple of days!) trying to track down the source of some crashes which ended up being due to the

[gmx-users] RE: NVT EQUILIBRATION

Keep the discussion to the emailing list please. How many molecules that is required you can calculate yourself. What is the density? You know the volume, therefore you can calculate yourself how many molecules should be in that space, simple calculation. You should also be able to eye ball

[gmx-users] Protein_model_refinement

Dear All I want to refine a protein homology model, I did minimization but then procheck does not give better Ramachandran plot. This model is a homodimer with each chain of 609 residue and a total of 1218 residue so a long MD simulation to search native state is not feasible. Can any one help me