Justin A. Lemkul wrote:
vferra...@units.it wrote:
No, is not working also in this case... probably the problem is with
my mdp files:
I would argue that it's the coordinates that are the problem. For
instance, compare the distances expected by the topology:
1 3 1 0.1758
1 4 1 0.1758
1 5 1 0.1758
2 3 1 0.233839
2 4 1 0.233839
2 5 1 0.233839
3 4 1 0.290283
3 5 1 0.290283
4 5 1 0.290283
with the actual distances found in the coordinate file:
1 3 1 0.177
1 4 1 0.177
1 5 1 0.174
2 3 1 0.240
2 4 1 0.235
2 5 1 0.235
3 4 1 0.282
3 5 1 0.290
4 5 1 0.289
The model requires 9 constraints to be satisfied in harmony. If the
starting geometry isn't perfect (or very close to it), there's probably
too much rearranging required to make the model work. Removal of the
explicit H probably yielded a set of constraints that could be somewhat
satisfied by EM, but fall apart in MD, which could be for a variety of
reasons.
I've obtained a stable trajectory for a single CHCL3 molecule. By setting
"continuation = no" (so that constraints are not solved before step 0) in the
em.mdp file, and then reducing nstlist to 5 in md.mdp, I was able to run 100 ps
of MD with no issue. The value of nstlist is probably the cause of the crash
you mention. Updating the neighborlist every 200 fs is 10-20 times too long.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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