[AMBER] Generating reservoirs for non-Boltzmann T-RREMD

From: Eugene Yedvabny <eyedvabny.berkeley.edu>
Date: Fri, 4 Oct 2013 12:50:42 -0700

Hello Amber community,

Is there any functionality in cpptraj or ptraj that enables easy reservoir generation and energy calculation to use in pmemd REMD with -rremd 2? Currently I am generating my reservoirs by parsing through mdout files and extracting EPtot values, followed by manually creating the header with the random seed. This is of course doable, if a little cumbersome when extracting energies from several MD runs into one reservoir. But my current project involves slightly modifying some of the force-field parameters, and I would need to recalculate the energies of my reservoir structures using this new prmtop. It seems the only way to do so presently would be to run Sander in analysis mode on all of my trajectories and then parse out the generated mdouts into another reservoir.

Since ccptraj can load many mdcrds and prmtops, it would be ideal to have a function that generates the reservoirs and savene files all in one go, akin to clusterdihedral function that is used for -rremd 3. Unfortunately I was not able to find a reference to any such function, or any function in cpptraj that would generate EPtot values for all mdcrd frames. Does anyone have a suggestions, or is my present multi-step process the only way to go about generating the reservoir?

Thank you,
Eugene Yedvabny

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Received on Fri Oct 04 2013 - 13:00:06 PDT
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