[gmx-users] free energy of removal of a molecule from the bulk
valentina.erastova at durham.ac.uk
Sun Mar 23 17:31:21 CET 2014
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.
Where am I going wrong?
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