On 2/12/13 5:44 PM, Sonia Aguilera wrote:
Thank you Justin,
So, your advice is not to perform the npt calculation and to run the md
after the nvt?
A common mistake is to think that there is a "standard" protocol that one must
follow. While it is true that for the condensed phase, a common procedure
involves restrained NVT and NPT prior to production simulations under an NPT
ensemble, this protocol is by no means necessary or appropriate under all
conditions. Simulating in vacuo requires different procedures and .mdp
settings. This topic has been discussed several times just in the last week or
two; please refer to the list archive for useful information.
-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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