[gmx-users] Fwd: Relative free energy perturbation

[Hannes Loeffler]

On Thu, 6 Jul 2017 09:17:18 +0200
Davide Bonanni <davide.bonanni at unito.it> wrote:

> I am apologize if I resend the same message but I forgot to change the
> object.
> 
> Dear Hannes,
> 
> Thank you very much for your reply, really appreciated.
> 
> 
> 
> > Date: Mon, 26 Jun 2017 12:09:45 +0100
> > From: Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk>
> > To: <gromacs.org_gmx-users at maillist.sys.kth.se>
> > Cc: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Fwd: Relative free energy perturbation
> > Message-ID: <20170626120945.75215167 at stfc.ac.uk>
> > Content-Type: text/plain; charset="US-ASCII"
> >
> > On Mon, 26 Jun 2017 12:25:19 +0200
> > Davide Bonanni <davide.bonanni at unito.it> wrote:
> >  
> > > 1) Can I perform the calculation in a single step with soft core
> > > potential enabled? I mean, is it correct to transform directly the
> > > hydrogen into a chlorine instead of using 2 topologys and 2
> > > complexes, where in the first step I transform the hydrogen into
> > > dummy atom, and in the second I transform the dummy atom into
> > > chlorine.  
> >
> > Technically speaking you can perfectly do that but in practice it
> > can be much more efficient to directly and linearly transform one
> > atom type into another (single topology approach).  There is no
> > need for a softcore potential in this case.  Those would only be
> > activated for atoms that either appear or disappear i.e. atoms with
> > zero vdW parameters.  The input and topology files from FEsetup
> > should be all you need.  
> 
> 
> Can I have problems if I keep active the softcore potential whether
> is not needed?

I don't think vdW softcores would be activated as said above. In any
case you can just sc-alpha=0 to switch softcores off all together.
Even if they were on, all that would happen is that you would choose an
alternative path (so need to be consistently used in the other leg(s)
of the thermodynamic cycle).  So you should get the same overall ddG
albeit in a possible less efficient fashion because you completely
decouple on atom while recoupling its counter-part.  It just doesn't
make sense to me to do it that way.

Cheers,
Hannes.