Re: [gmx-users] VMD

Hi Rahul, VMD ran out of memory. Try using trjconv to create a new xtc with a subset of atoms or a subset of frames. Best wishes James > I tried to visualize my xtc on VMD and the job get killed at 7000 frames > > why is that so? > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* >

[gmx-users] VMD

I tried to visualize my xtc on VMD and the job get killed at 7000 frames why is that so? -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] dihedral MM scan

Hi Justin, Sorry, I am just doing some dihedral population analysis to see which part is wrong. I agree. Most likely I am making some mistakes which is hidden to my eyes. I will prepare and share those with you with the result of population analysis when prepared. Cheers Mohsen On Thu, Jan 19,

Re: [gmx-users] Dihedral Population Analysis -Index file

Thanks Mark. That is great. I tried that and I made an Index file of what I want. "DIH" resname DOPC and atomname O C12 C23 C However, looking at index files, the order of atom numbers is not right and give me a wrong dihedral for analysis with g_angle. 8101 8116 8117 8126 *I want it

[gmx-users] Excluded Volume Effect

Hi All, I want to calculate the excluded volume effect on a protein's dynamics from a protein-in-water trajectory. I used the following command to calculate the volume g_sas -s md.tpr -f md.trr -tv volume.xvg -probe 0 The output file (volume.xvg) has 3 columns - 1st column is time, 2nd

Re: [gmx-users] velocity generation in Gromacs 2016

On 1/24/17 10:42 AM, Kukol, Andreas wrote: Hello, I always used to generate velocities for an MD run in the equilibation step by setting gen-velyes in the mdp-file. In the sample mdp-file for Gromac 2016, this option is not set. Does it mean velocities are now generated by default ?

[gmx-users] velocity generation in Gromacs 2016

Hello, I always used to generate velocities for an MD run in the equilibation step by setting gen-velyes in the mdp-file. In the sample mdp-file for Gromac 2016, this option is not set. Does it mean velocities are now generated by default ?

Re: [gmx-users] Having WCA bonded interaction with FENE potential

Hi, Sounds like one approach might be to use FENE bonds, normal exclusions = 3 (or whatever), and to add [ pairs ] function type 1 for each bonded interaction, and thereby implement your WCA. But these approaches might differ in how VDW interactions between atoms separated by more than one bond

[gmx-users] Having WCA bonded interaction with FENE potential

Hello, I am simulating a charged bead-spring modelled polyelectrolyte with FENE bond stretching potential and Deby Huckel potential for electrostatics. I need to combine FENE bonded interaction combined with WCA potential, otherwise the beads overlap with each other since there is no replusive

Re: [gmx-users] GPU file

gmx mdrun -rerun md.xtc deffnm md in my cpu. Hope this will get me the necessary file. Isnt it? On Tue, Jan 24, 2017 at 4:10 PM, Mark Abraham wrote: > Hi, > > As the md.log file reports, energy groups aren't implemented on GPUs. You > can use > > mdrun -s topol.tpr

Re: [gmx-users] Dihedral Population Analysis -Index file

Hi, On Tue, Jan 24, 2017 at 12:35 AM Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Dear Gromacs users, > > I have a trajectory file which I wish to do a dihedral analysis for > specific dihedral. > Based on what I understood from mailing list and manual, I made an > index.ndx

Re: [gmx-users] simulation of ternary complex

Dera Maria, Yes that is possible. Be sure to make a good choice of forcefield, so that you have decent parameters for all molecule types in your simulation. Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC

Re: [gmx-users] GPU file

Hi, As the md.log file reports, energy groups aren't implemented on GPUs. You can use mdrun -s topol.tpr -rerun traj.trr -nb cpu to get them for the frames you saved. Mark On Tue, Jan 24, 2017 at 10:54 AM RAHUL SURESH wrote: > Why is that ENERGY is 0 when simulation

Re: [gmx-users] simulation of ternary complex

I want to simulate ternary complex of protein -DNA -ligand..Is it possible to simulate it combinely? Yeah sure, you can, your order might be protein-DNA-ligand during topology development and gro file format good luck On Tue, Jan 24, 2017 at 2:25 AM, maria khan

[gmx-users] simulation of ternary complex

Dear gromacs Users.. I want to simulate ternary complex of protein -DNA -ligand..Is it possible to simulate it combinely? secondly..Gromacs has no graphical interface to visualize results..how can we resolve this issue..Using VMD i have some issues regarding trajectories.. Regards.. Maria

[gmx-users] GPU file

Why is that ENERGY is 0 when simulation is from GPU. and how to get the energy file by running in in cpu -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] How to concatenate tpr files?

Dear Leila, The RMSD is, by default, calculated with respect to the coordinates in the tpr file, which is why you get different results with different tprs. Which one to choose depends on exactly what you want to measure. Kind regards, Erik __ Erik Marklund, PhD