[AMBER] how long should a NPT equilibrium take in QM/MM MD?

From: <guoyu1.shanghaitech.edu.cn>
Date: Tue, 13 Nov 2018 01:17:56 +0000

Dear everyone,

   I'm trying to run a QM/MM umbrella sampling with amber.
   In the AMBER Advanced Tutorial 17 for umbrella sampling, the author first run a 2000 step minimization then a 50ps NPT equilibration before production run.
   But my QM region include 80 atoms, 50ps NPT equilibration would cost me a long time if I use DFT method. So in a attempt I make, I only run a 1ps NPT equilibration with PM6DH+. Although I got what I want, but I do not know if I'm making mistake shorten the NPT run.

   So, my question is, before a QM/MM MD production run, can I just run a minimization and NPT equilibration as in http://ambermd.org/tutorials/advanced/tutorial17/section2.htm ? If I can, how long should a equilibration run take? If I can not, what procedure should I take?
   I'd be very thankful if anyone can answer my question or tell me where to look for the answers.
   Thanks for reading.

   best wishes,
   Yu
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Received on Mon Nov 12 2018 - 17:30:02 PST
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