[gmx-users] Can we calculate rmsd from after energy minimization?

Mark Abraham mark.j.abraham at gmail.com
Mon Dec 1 08:40:15 CET 2014

On Mon, Dec 1, 2014 at 7:19 AM, Seera Suryanarayana <palusoori at gmail.com>

> Dear Gromacs Users
> I would like to know whether  it possible to calculate rmsd immediately
> after energy minimization step, in other words from em.tpr and em.trr file.
> I tried to calculate the rmsd by using above mentioned files, but I have
> got nothing.

That's what we have, too. :-) What was your exact command and what did you
get as output?


If it is possible to calculate the rmsd from the energy minimized
> structure, kindly tell me how do we do it.
> Thanks in advance
> Surya
> Graduate student
> India.
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