[gmx-users] tabulated non-bonded potentials with replica exchange (potentials that change with temperature)

[Mark Abraham]

On Mon, Jan 19, 2015 at 12:39 AM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> Dear Users:
>
> I presume that I can use tabulated non-bonded potentials with replica
> exchange in gromacs 4.6.7.


Indeed, I can think of no reason why not (modulo that there's only support
for those in the group scheme).


> However, my question is whether it is possible to supply different tables
> for each of the different temperatures?
>

Can't think of a reason why or why not. I would be more hopeful of the
mdrun -multidir implementation (because that basically does a "cd" at the
start of mdrun, so it doesn't need all the table filenames to have been
suffixed correctly, they just need you to organize them correctly).


> My actual use involves the plumed plugin to do hamiltonian replica
> exchange. With that patch it is possible to modify the .tpr files for each
> ensemble prionr to calling mdrun and have gromacs mdrun compute exchange
> energies properly. However, since tables are sent to mdrun directly from
> the command line, rather than through the .tpr file, my guess is that there
> is no way to load in a separate tabulated potential for each ensemble.
>

Embedding table files in the .tpr is on the to-do list for implementing
tables in the Verlet scheme.

Mark


>
> Thank you for your insight,
> Chris.
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