[gmx-developers] Easy Access to MDrun Functions

[Groenhof, Gerrit]

Hi, 

Now I understand better and I had a quick look at the papers as well.

>From the papers, however, in infer a different coupling scheme as the one you suggest in the email.

Following the protocol in the papers, you'd like to have a number of snapshots of the solvent molecules at a fixed configuration of the solute and use these to compute at the QM/MM level the interaction energy between QM solute (or solute fragments) and the MM solvent molecules. In that case you can perform a simulation with fixed silute, extract snapshots from the trajectory and perform single point QM/MM simulations on them to get the interaction energy.

>From your email i infer you want instead of snapshots have some time averaged potential. I assume you mean ensemble averaged? Which can be obtained by averageing over the snapshots (as also done in the papers I think).

I think the difficulties will arise when your wave packet starts branching into different electronic states near the conical intersection. What electrostatic field would the solvent have to feel in order to react appropriately to the superposition of electronic states?

Furhtermore, I am not sure, but feel that the back coupling from the wave packet QD region to the classical MM region is not yet consistent in your approach. The wave packet will smear, so that also the solvent molecules should feel smeared atoms (important for both Coulomb and LJ), rather than point charges of the solute during their MD simulation. But perhaps that does not matter?

Anyways, I think the QMMM code may help you. At least I hope it can save you time and effort.

Best,

Gerrit




________________________________________
From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] on behalf of c3633 [c3633 at cup.uni-muenchen.de]
Sent: Wednesday, August 10, 2016 11:52 AM
To: gmx-developers at gromacs.org
Subject: Re: [gmx-developers] Easy Access to MDrun Functions

Hi Gerrit,

I actually didn't include to much detail on the theory in the original
e-mail, because the questions were more about the technical stuff. So
here is a briefer description of what we're doing:

We're calculating wavepacket dynamics on a precalculated potential
energy surface that should include all intramolecular interaction, to
which a time-dependant Ehrenfest-Potential from the surrounding
environment is added. Since every point on this surface corresponds to
an arrangement of atoms in real space, the added Potential is equal to
the solute-solvent interaction energy of that particular arrangement at
each time-step, which can be easily calculated in gromacs at each
time-step for each surface point.
For a time independent potential, see these publications: J. Chem.
Theory Comput., 2015, 11 (5), pp 1987–1995 or
http://dx.doi.org/10.1063/1.4941600.
If you want to gain a effect of the solute on the solvent, you also
calculate the forces (in addition to the potential energies) for each
point at each time step and propagate the molecules classically with the
density-weighted sum of the forces while constraining the solute
appropriately, to exclude the movement already treated with quantum
mechanics, which i also would like to do using gromacs functions.

I hope that clarifies my original questions.
Best,
Martin.


Am 09.08.2016 12:49, schrieb Groenhof, Gerrit:
> Hi Marten,
>
> Because it is not totally clear to me yet what you want to do, i am
> not sure if I can help.
>
> I understand you want to do a QM simulation, using wave packet
> dynamcis? This would require more information on the (presumably
> QM/MM) potential energy surface than the on-the-fly forces?
>
> Or is it an Ehrenfest approach, which requires you to apply the
> expectation value of the QM/MM forces on the MM atoms?
>
> Or do you want to do Newtonian dynamics on a QM/MM potential energy
> surface, either on the-fly, or use a effective (averaged) MM
> environment
>
> The latter would be the easiest, but I am not sure if that's what
> you're talking about.
>
> BEst,
>
> Gerrit
>
> ________________________________________
> From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se
> [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] on behalf of
> c3633 [c3633 at cup.uni-muenchen.de]
> Sent: Tuesday, August 09, 2016 11:10 AM
> To: gromacs.org_gmx-developers at maillist.sys.kth.se
> Subject: [gmx-developers] Easy Access to MDrun Functions
>
> Hi,
>
> I am currently developing on a quantum dynamics C++-program and I would
> like to use the gromacs library to treat the environment of my system
> within a molecular dynamics framework. The current approach is to write
> an mdrun-like function that, during one time-step to first calculate
> forces on the environment-atoms and to modify them according to what
> happens in the quantum-dynamics and the to propagate the System
> according to those forces. I am fairly new to gromacs and I am just
> starting to understand the library. The functions I would need for my
> program seem to be do_force() and update_coords() from the
> legacyheaders.
> I would like to ask first, if there is a easier way to approach this,
> probably through modules like it is done for data analysis? And if not,
> how does one best generate input for those functions from a gromacs
> input file?
>
> Thank you very much for your time,
> Martin
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