[gmx-users] free energy of removal of a molecule from the bulk

Mark Abraham mark.j.abraham at gmail.com
Sun Mar 23 23:40:59 CET 2014

On Sun, Mar 23, 2014 at 5:30 PM, Valentina
<valentina.erastova at durham.ac.uk>wrote:

> I am running thermodynamic integration and I wanted to remove 1 molecule of
> water from bulk (as a test). But I am not sure how to specify it in the map
> file with couple-moltype:
> If I specify SOL I will be decoupling all of it, if I rename that specific
> molecule to something else, I get:
> The [molecules] section of your topology specifies more than one block of
> a [moleculetype] with a [settles] block. Only one such is allowed. If you
> are trying to partition your solvent into different *groups* (e.g. for
> freezing, T-coupling, etc.) then you are using the wrong approach. Index
> files specify groups. Otherwise, you may wish to change the least-used
> block of molecules with SETTLE constraints into 3 normal constraints.
> That is fair enough, but making index group and specifying the group r_570
> in the couple-moltype doesn't really work.

Dunno what "doesn't really work" means, but if couple-moltype insists on a
whole moleculetype, then you need to create a second water moleculetype and
use normal constraints, rather than [settles], like the error suggests.


> Where am I going wrong?
> Thank you,
> V
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