[gmx-users] energy minimization

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 12 02:46:13 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 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

Well, you've satisfied the EM criteria.  Fmax is indeed less than 1000.  This 
doesn't seem to be problematic.


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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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