From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Oct 15 2013 - 10:44:51 CDT
In general, it is simpler to setup the complete "dual topology" system from the beginning, then add solvent and other components.
----- Original Message -----
> Hello Jerome,
> Thank you very much for your reply.
> Ok, so I should use the equilibrated system for lambda=0 (this is where I
> want to start). To this I can add the appearing atoms (lambda=1) also after
> the equilibration run and then create the .fep file and so on.
> Initially, I was trying this approach, one difficulty I faced was how to
> number the atoms after 99999.
> For example, when I add the appearing atoms to the pdb file (lambda=0 )
> after equilibration, the seriel numbers change. This problem arises from
> the water molecules. Maybe another option would be just to select
> everything except water (for lambda=0 after equilibration) and add
> appearing atoms and then solvate the system? Is this approach correct?
> thanks again for your help,
> On Mon, Oct 14, 2013 at 3:32 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> > Hi Shyno,
> > There seems to be something wrong with your approach. If you do an
> > equilibration run prior to the FEP, you should do that at a well-defined
> > lambda state, by enabling the alchemical options and setting lambada to
> > either 0 or 1, depending on where you want to start from.
> > Cheers,
> > Jerome
> > ----- Original Message -----
> > > Dear all,
> > > I am doing FEP calculations. For my system, I am mutating more than 1
> > > residue at the same time (all are same type of mutations). Since this is
> > my
> > > first time doing free energy calculations, I am trying to set up the
> > system
> > > as mentioned in the tutorial:
> > > "A tutorial to set up alchemical free energy perturbation calculations in
> > > NAMD"
> > > As the first step, I am writing the .fep input file which contains all
> > toms
> > >
> > > (appearing, disappearing and non-changing atoms). Initially, I was doing
> > > FEP immediately after minimization. However it wasn't running. So I did
> > a
> > > short run (about 3 ns) after minimization. Then submitted FEP runs, this
> > > worked. I would like to confirm this approach is correct.
> > >
> > > When I did the short run (3 ns), the system has both disappearing and
> > > appearing atoms. For eg. the hydrogen attached to a carbon atom will
> > > disappear and a methyl group will appear. In my system I have both
> > hydrogen
> > > and methyl atom bonded to the carbon atom at the same time during the 3
> > ns
> > > run. Is this approach correct?
> > > Any help will be appreciated,
> > > thanks,
> > > Shyno
> > >
> > >
> > > --
> > > Shyno Mathew
> > > PhD student
> > > Department of Chemical Engineering
> > > Columbia University
> > >
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University
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