Vitaly V. Chaban wrote:
1. No problem at all in vacuo? That with a 1 fs timestep and the sd
integrator? Strange then that your molecule is ok and the water is ok,
but they are unstable together. Perhaps your'e not getting any LJ
interactions (or not correct ones) between your solute and water? That's
where I would focus my efforts if I was you. I suppose it could also be
solute-solute LJ problems...
If I switch off electrostatics between CIP and water, the problem
disappeared... Maybe it's really worth to use a smaller timestep for
this system ...
Can you post your .mdp file?
-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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