[gmx-developers] dhdl expanded ensemble

[Berk Hess]

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.

Cheers,

Berk

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