Dear Justin, I want to get energy per residue not time. if i use mdrun -rerun with energygrps in md.mdp then g_energy i obtain enery per time not residue. at last, i don't understand how to get Energy per residue .
Best wishes, Afsaneh > afsaneh maleki wrote: > >> Dear gromacs users, >> Is there a way to get energy values (Vdw,..) per residue at the end of MD >> prosses? >> >> > > Yes and no. You won't be able to get, for instance, the absolute van der > Waals energy of a residue. That doesn't really make any sense, since vdW > interactions take place between particles. There may be some 1-4 type > interactions within a residue that you could quantify, but not much else. > > You can decompose short-range residue-residue energies using energygrps in > the .mdp file, and re-running the trajectory with the new .tpr file (mdrun > -rerun), but the .edr file can quickly get out of hand in terms of disk > usage, depending on how many groups you have (since you will then have > essentially N^2 energy terms to write out, where N is the number of > energygrps). > > -Justin > > > I would really appreciate any help. >> >> Afsaneh >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >
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