[gmx-users] Coupling only a variable solvent subgroup to the thermostat

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 26 21:58:44 CET 2013

Only your kind of scripting approach will be able to do this. While we do
plan to provide this kind of "dynamic selection" for the analysis tools in
5.0, I'd be surprised if we found time/need to do it for mdrun.

Whether it's a useful thing to do, I have no real idea.


On Mon, Feb 25, 2013 at 3:51 AM, Leandro Bortot <leandro.obt at gmail.com>wrote:

> Dear GROMACS users,
>      In a NPT molecular dynamics simulation of a system composed by a water
> box with ions and a protein I want to couple only water molecules which are
> far from the protein to the Nosé-Hoover thermostat and leave the remaining
> system uncoupled.
>      I managed to couple a subset of the solvent molecules by specifying a
> group in the mdp under tc-grps and by giving an index file to mdrun. The
> problem is actually how to create the appropriate (variable) selection of
> the water molecules which are to be coupled to the thermostat.
>      While probably an inefficient way of doing this, I can only think of a
> script which (1) stops the simulation just before the thermostat acts over
> the system; (2) makes the index file with the appropriate selection with
> g_select and then (3) continues the simulation, allowing the thermostat to
> act over the appropriate subset of the solvent.
>      I'm currently using 5 ps as the period of the contact between the
> system and the thermal bath, meaning that I would have to stop the
> simulation, say, each 4.9ps in order to make the new index file. Actually,
> this is probably overcautious since I don't think the waters will move so
> much in 5ps. Maybe I can make a new index file each, say, 20ps.
>      Any suggestions and/or comments about how to do this and my proposed
> script would be very helpful.
> Thank you in advance,
> Leandro Bortot
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