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.
-Justin
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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