From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Oct 15 2013 - 11:29:51 CDT
Sorry, there was a misunderstanding. Then what you were doing seems correct, and I don't know why it didn't run properly.
Jerome
----- Original Message -----
> thanks again for your reply. Sorry for asking more questions. Please bear
> with me as I explain few details:
> This is exactly what I did. The dual topology was made in the beginning (i
> used non equilibrated systems to make it). Then added counterions and
> water. After this the dual topology system was minimized and submitted for
> a short run before FEP calculations. As mentioned before, for this short
> run, the system has both hydrogen (disappearing atom) and methyl group
> (appearing) bonded to the carbon atom at the same time during the 3 ns run.
>
> Or you meant to say the dual topology has to be made using the equilibrated
> systems?
>
> thanks again,
> Shyno
>
>
>
> On Tue, Oct 15, 2013 at 11:44 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
> > In general, it is simpler to setup the complete "dual topology" system
> > from the beginning, then add solvent and other components.
> >
> > Jerome
> >
> >
> > ----- 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,
> > > Shyno
> > >
> > >
> > >
> > > 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
> > >
> >
>
>
>
> --
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University
>
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