[gmx-users] a question related to gmx energy minimization

[Tsjerk Wassenaar]

Hi Brett,

Too high for what?

You do EM because you just built (part of) your system, and in doing so
introduced clashes and non-ideal geometries. These lead to high potential
energy, so you relax them with EM. What you see is how much the system
relaxed. Noone usually cares how much potential energy was lost during EM.
The thing that matters is whether the resulting system is relaxed enough to
run the simulation.

Cheers,

Tsjerk

On Sun, Apr 26, 2015 at 2:43 PM, Brett <brettliu123 at 163.com> wrote:

> Dear All,
>
> I just run the command gmx energy -f em.edr -o potential.xvg for my energy
> minimization step MD, but I find the RMSD given by this command is 142611,
> which I regard to be too high.
>
> Will you please explain to me what leads to the so high RMSD (Err.Est is
> 53000, Tot-Drift is -341107 KJ/mol)?
>
> I am looking forward to getting your reply.
>
> Brett
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-- 
Tsjerk A. Wassenaar, Ph.D.