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

Valentina 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? 
Thank you, 

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