Re: question about setting up FEP calculations

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Mon Oct 14 2013 - 20:01:48 CDT

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, Jrme Hnin <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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