[gmx-users] tutorial for "dual" alchemical transformation in gromacs?

hannes.loeffler at stfc.ac.uk hannes.loeffler at stfc.ac.uk
Sun Nov 29 14:36:38 CET 2015

Practical question: why would you want to do that?  Your two molecules will drift apart unless parts of the molecules are linked together in a "single" topology fashion or or you introduce other restraints/constraints.

In practice, you can do that with Gromacs relatively easily.  The manual describes how to set up the A and the B state of a molecule.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Sebastian Stolzenberg [s.stolzenberg at fu-berlin.de]
Sent: 29 November 2015 13:11
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] tutorial for "dual" alchemical transformation in   gromacs?

Dear Gromacs experts,

I am looking for a Gromacs tutorial to perform a "dual" alchemical
transformation in a water box, i.e. a mutation or any other alchemical
transformation, in which:
the nonbonded interactions between the environment and a molecule A
disappear as lambda goes from 0 to 1, and
the nonbonded interactions between the environment and a molecule B
appears simultaneously.
Interactions between atoms A and B are to be excluded.

So far, I have been trying to use the Gromacs user guide to extend the
ethanol tutorial
into such a "dual" transformation, but also because I am currently faced
with manually manipulating my topology file, this option is highly prone
to my own errors.

Would you be able to help?

With Thanks and Best Regards,
Gromacs Users mailing list

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