From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Tue Oct 15 2013 - 11:21:51 CDT
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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