Dear Hannes, Thank you very much for your reply, really appreciated.
> 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-ID: <20170626120945.75215...@stfc.ac.uk> > Content-Type: text/plain; charset="US-ASCII" > > On Mon, 26 Jun 2017 12:25:19 +0200 > Davide Bonanni <davide.bona...@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? > > 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. Cheers, Davide Bonanni -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.