[gmx-developers] dhdl expanded ensemble

Shirts, Michael R. (mrs5pt) mrs5pt at eservices.virginia.edu
Fri Aug 28 14:58:49 CEST 2015

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
>> enerd->term.
>> 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.
>> Best,
>> ~~~~~~~~~~~~
>> 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
>> Hello,
>> 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.
>> -ChrisM
>> Mirabzadeh, Christopher
>> Graduate Research Assistant/Physics Instructor
>> Department of Physics
>> University of Idaho
>> Moscow, Id
>> (509)339-5647

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