[gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 165

Davide Bonanni davide.bonanni at unito.it
Wed Jul 5 17:09:19 CEST 2017

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

> > 2) Referring to BevanLab Tutorial 6: Free Energy Calculation (
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm
> > x-tutorials/free_energy/index.html), I have to perform every step of
> > molecular dynamics at every Lambda value, is that right?
> Yes, you will need to do a simulation for every and each lambda step.
> > 3) I run a test minimization step (mdp file attached) of my complex
> > at the last "init-lambda-state", 15 in my case. Looking at the .trr
> > output file I can see that the bond between the carbon and the
> > hydrogen which should be trasformed is longer than a normal C-H bond,
> > but the atom is still recognized as hydrogen (picture
> > "http://tinypic.com/r/2wp11dh/9": purple -> init-lambda-state = 0 ;
> > blue -> init-lambda-state = 15). I was wondering if this is what I am
> > supposed to see, so if gromacs is considering the state B of my
> > system where I have chlorine bound to carbon instead hydrogen.
> What does "recognized as hydrogen" mean?  I suspect that what you are
> referring to is the output of some visualisation program because you
> instructed it to interpret that particular atom to be a hydrogen.
> What you need to expect to see is that a C-H bond is transformed into a
> C-Cl bond and accordingly the bond length increases.

Of course, It's like you said. I see the bond length to increase as in the
img "http://tinypic.com/r/2wp11dh/9".
Thank you again.


Davide Bonanni

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