RE: [gmx-users] Temperature Histogram

Thank you for your answer. However, when I use g_energy on .edr file it prints the average temperature of the system and not of the group of atoms that I am interested in, which is why I was trying to make g_traj work cos it uses index.ndx file for choosing the segment from your system and calc

[gmx-users] Force vs distance plot in pulling simulation?

But be aware that the force depends on the pulling velocity. If you perform the simulation with two different pulling velocities you'll get two different forces for each distance. The easiest way to get the force as a function of the distance (without the bias of the pulling velocity) would be t

[gmx-users] (no subject)

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Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

On 2012-11-18 10:40, Atila Petrosian wrote: Dear David Thanks for your attention. I have 2 problems/questions: 1) There are a specific orientation for GLN ligand with regard to protein in my system. If I do what you said [you make a separate molecule Gln-Ala using pymol or vmd], specific orien