[gmx-developers] dhdl expanded ensemble
Mirabzadeh, Christopher (email@example.com)
mira2978 at vandals.uidaho.edu
Fri Aug 28 18:17:47 CEST 2015
Thank you! I will look into redmine and I will also look at those variables closer.
Graduate Research Assistant/Physics Instructor
Department of Physics
University of Idaho
> On Aug 28, 2015, at 5:58 AM, Shirts, Michael R. (mrs5pt) <mrs5pt at eservices.virginia.edu> wrote:
> Yeah, apologies, checking 5.1 in the in the debugger for a binding free
> energy change, then there are some differences between the dhdl output
> file when nstdhdl = 20, and the terms in the enerd->term dhdl components
> at step = 10 matched what the output was in the dhdl file when nstdhdl =
> 10. So don't rely on that dhdl, since it is missing some terms.
> In any case, it would be relatively easy to change the existing machinery
> to force it do the full calculation dhdl calculation every step. If you
> wanted to make it very easy, just set nstdhdl = 1, and introduce a new
> variable that controls the printing of dhdl to the file alone.
> Michael Shirts
> Associate Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434) 243-1821
> On 8/28/15, 3:11 AM, "Berk Hess" <hess at kth.se> wrote:
>> No. To be more precise dhdl is only (fully) calculated at each step
>> where free energies are calculated, i.e. every nstdhdl steps.
>> To find where the final values are stored, it's often easiest to look in
>> mdebin.c, in this case at line 1244.
>> On 2015-08-28 03:52, Shirts, Michael R. (mrs5pt) wrote:
>>> 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
>>> 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
>>> calculated and I see in mdebin.c there is a line that says "/* store_dh
>>> dE */". Is the derivative "store_dhdl=enerd->term[F_DVDL]"?
>>> Or, is this already being called somewhere in expanded.c that I can
>>> 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
>>> 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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