[gmx-users] energy minimization

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 12 03:06:25 CEST 2009

Jamie Seyed wrote:
> Dear all,
> I performed an md simulation but it crashed at the beginning because
> according to it "system was exploding". Also when I tried to see the system
> by ngmx, there was no water anymore and it was only the molecule sitting in
> the box(after grompp and before mdrun it was a box of water plus the
> molecule)!!??

So you used a wrong file at some point... name your files carefully, and 
use them carefully.


> So from the information that I found in the mailing list I tried to do
> energy minimization step only for my system in vacuo. Obviously it was fine,
> however I got these results:
> ---------------------------------
> Steepest descents converged to Fmax < 1000 in 64 steps
> Potential energy = 1.9027975e+04
> Maximum force  = 6.3652850e+02 o atom 88
> Norm of force     = 1.6029111e+02
> ---------------------------------
> So my question is should I continue with this potential energy or what.
> Please give me some suggestions?? Many Thanks in Advance/Jamie
> ------------------------------------------------------------------------
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