[gmx-users] couple-moltype question

Fabian Casteblanco fabian.casteblanco at gmail.com
Tue Apr 3 17:16:14 CEST 2012

Hello Gromacs community,

I am trying to simply decharge a part of large molecule.  I know from the
tutorial we can use 'couple-moltype' along with 'couple-lambda0', etc, but
in this case I simply change the topology to state A and then I have state
B written with no charges since I'm only doing a piece of the molecule.  I
have a free energy but it is only the free energy including interactions
between the piece of the molecule and surrounding solvent.  I see
'couple-intramol' is an option to have intramolecular interactions also
decoupled but it requires a 'couple-moltype' to be set.  Is there any way I
can set that variable to simply a piece of a molecule?

Thank you in advance for your help.

Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering
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