On 1/6/13 12:33 AM, Shima Arasteh wrote:
Do you mean that I re-run NPT step with the new index file and npt.gro (which I
got from the last NPT equilibration)? That's not clear to me yet.
That's where I'd start. You may have to run the new configuration through the
entire equilibration protocol, though. Instability during MD often indicates
inadequate equilibration, so whatever your protocol is may not be sufficient as
is and may require greater time.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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