Re: [gmx-users] Fwd: Relative free energy perturbation

; Date: Mon, 26 Jun 2017 12:09:45 +0100 > > From: Hannes Loeffler <hannes.loeff...@stfc.ac.uk> > > To: <gromacs.org_gmx-users@maillist.sys.kth.se> > > Cc: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Fwd: Relative free energy perturbation > > Message-I

Re: [gmx-users] Fwd: Relative free energy perturbation

aillist.sys.kth.se> > Cc: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Fwd: Relative free energy perturbation > Message-ID: <20170626120945.75215...@stfc.ac.uk> > Content-Type: text/plain; charset="US-ASCII" > > On Mon, 26 Jun 2017 12:25:19 +0200 > Davi

Re: [gmx-users] Fwd: Relative free energy perturbation

On Mon, 26 Jun 2017 12:25:19 +0200 Davide Bonanni 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,

[gmx-users] Fwd: Relative free energy perturbation

Hi, I am trying to perform an alchemical free energy perturbation with gromacs, since I am approaching this technique for the first time. So, it would be so nice if you could help me to clarify some doubt. I have built my system, which is composed of 1 protein, 2 cofactors, and 1 ligand that