Dear
Amber developers and users
I generated a charged nanodroplet by carving an octahedron FB4 water box
surrounding a peptide and multiple Na+ cations. I minimized this spherical
system in vacuum. Now my goal is to perform MD simulation (in vacuum) at
constant temperature and sample the trajectory as the water molecules leave
the nanodroplet (the simulation will stop every 100 ps to remove the water
molecules that are outside a desired radius, r). After removal of all water
molecules, the simulation will continue for 250 ns. Based on this system, I
would like to use Nose-Hoover chain (NHC) method for the first part of the
simulation where the water molecules are present and the langevin dynamics
after removal of (almost) all water molecules, to control the temperature
through the simulation. Now my question is what is the exact value for ntt
parameter in Amber16 that allows me to use NHC thermostat? If it doesn't
exist, can I use the modified ensemble (OIN) with ntt=9 or do I have to
perform the whole simulation in NVE (ntt=0) instead? Any help would be
greatly appreciated.
Best Regards
sam
--
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
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Received on Fri Jan 20 2017 - 13:00:03 PST
