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

From: Niel Henriksen <>
Date: Fri, 4 Oct 2013 13:25:18 -0700


I don't think there is any "all-in-one" tool to do what you are asking.
 The multi-step process is what I have used.

Unless I misunderstand you, you seem to be using potential energies (from
the mdout file) and coordinate frames from the SAME simulation.
 Unfortunately, the printed potential energies do not correspond to the
written frames in the mdcrd file. (see ) So you probably need to do
the Sander-in-analysis-mode step regardless of what your plans are.


On Fri, Oct 4, 2013 at 12:50 PM, Eugene Yedvabny <>wrote:

> 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
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Fri Oct 04 2013 - 13:30:03 PDT
Custom Search