[AMBER] Extracting temperature-based potential energies from REMD

From: Lee-Ping Wang <leeping.stanford.edu>
Date: Mon, 25 May 2015 09:44:10 -0700

Hi everyone,

I’ve been running some replica exchange simulations in Amber. I’ve got a simple script for cpptraj (adapted from the tutorial at http://ambermd.org/tutorials/advanced/tutorial7/ <http://ambermd.org/tutorials/advanced/tutorial7/> ) for processing the output trajectories, resulting in “temperature-based” trajectories where the temperature is constant but the conformations jump around. The simulations are running very nicely; thanks for writing a great software package.

My question is how I could get potential energies to “go with” these trajectories? I would like to use these potential energies as input to a WHAM / MBAR calculation to improve the estimation of thermodynamic properties at each temperature.

My simple script is attached below.


- Lee-Ping

parm ../prmtop
ensemble ../remd.00/netcdf.00
ensemble ../remd.01/netcdf.00
ensemble ../remd.02/netcdf.00
strip :WAT
trajout pro.netcdf netcdf
trajout pro.pdb pdb start 1 stop 1

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Received on Mon May 25 2015 - 10:00:02 PDT
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