[AMBER] aMD and scaled MD simulation-NVT production runs

From: Neha Gandhi <n.gandhiau.gmail.com>
Date: Mon, 22 Jun 2015 14:24:25 +0800

Dear List,

I have seen papers on on aMD, Scaled MD and at times REMD where final
system equilibration wis done in isothermal–isovolumetric (NVT) ensemble
followed by 400 ps NPT run to ensure that the water box of simulated
systems had reached the appropriate density. Then, production simulations
were performed in the NVT ensemble.

I would like to know more about ensemble switch to NVT from NPT during
production? Can we start NVT run from with the last frame using the average
density from NPT (langevian thermostat)? How do I take care of the volume,
density and pressure while changing the ensemble?

Thank you
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Research Gate
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Received on Sun Jun 21 2015 - 23:30:02 PDT
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