[gmx-developers] dhdl expanded ensemble

Shirts, Michael R. (mrs5pt) mrs5pt at eservices.virginia.edu
Fri Aug 28 03:58:26 CEST 2015

Dhdl is automatically calculated at every step if free energies are
calculated. Look in sum_dhdl -- difference components are stored in

Unless it's a new development you would rather keep private for now, you
should consider posting the proposed enhancement on redmine.  You would
likely get some tips about how to do it in a way that could be more easily
included in later gromcs versions.

Michael Shirts
Associate Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434) 243-1821

From:  <Mirabzadeh>, "Christopher   (mira2978 at vandals.uidaho.edu)"
<mira2978 at vandals.uidaho.edu>
Reply-To:  "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
Date:  Thursday, August 27, 2015 at 12:20 PM
To:  "gromacs.org_gmx-developers at maillist.sys.kth.se"
<gromacs.org_gmx-developers at maillist.sys.kth.se>
Subject:  [gmx-developers]  dhdl expanded ensemble


What I'm trying to do;

I'm attempting to add functionality to expanded ensemble.

What I've done so far;

I've added functionality to accept my mdp options and found pre-written
functions to take advantage of.

Where I'm stuck;

I need the derivative of the Hamiltonian with respect to lambda at every
md step. I'm having a hard time narrowing down this variable. I know it's
calculated and I see in mdebin.c there is a line that says "/* store_dh is
dE */". Is the derivative "store_dhdl[]=enerd->term[F_DVDL]"?
  Or, is this already being called somewhere in expanded.c that I can take
advantage of, maybe dfhist?

Is the dhdl automatically calculated? Where is it stored? If dhdl isn¹t
being calculated automatically, is there an mdp option or mdrun flag that
I need?

I appreciate any advice that can be offered.


Mirabzadeh, Christopher
Graduate Research Assistant/Physics Instructor
Department of Physics
University of Idaho
Moscow, Id

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