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

[hannes.loeffler at stfc.ac.uk]

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
http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf
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,
Sebastian
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