Re: question about setting up FEP calculations

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Wed Oct 16 2013 - 16:21:09 CDT

Thanks again Jerome.
As you said I ran alchemify first on the psf file. Here is the output info
I got:

~/Alchemify/alchemify_LINUX 05collab_wet.psf out.psf 05collab_wet.fep

FEPfile : 112454 atoms found, 10 initial, 40 final
69937 angles : removing 0 angles coupling initial and final groups
57708 dihedrals : removing 0 dihedrals coupling initial and final groups
3932 impropers : removing 0 impropers coupling initial and final groups
Writing 400 exclusion pairs

Then I tried running FEP calculations. But I am still getting the following
error:

Reason: FATAL ERROR: Low global exclusion count! System unstable or
pairlistdist or cutoff too small.

FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html

Charm++ fatal error:
FATAL ERROR: Low global exclusion count! System unstable or pairlistdist
or cutoff too small.

I tried playing with cutoff distance!

thanks again for your help,
Shyno

On Tue, Oct 15, 2013 at 1:00 PM, Jrme Hnin <jerome.henin_at_ibpc.fr> wrote:

> No, that short run is not correct, because it does not describe any
> physically meaningful state.
>
> Now I suspect one thing: that the two end-point groups are clashing, and
> that causes instability. The only reason why that could happen is if you
> don't have the proper nonbonded exclusions, which could happen if you are
> running the memory-optimized version of NAMD.
>
> To make sure, you could try running Alchemify on your PSF before running:
> http://www.edam.uhp-nancy.fr/Alchemify/
>
> Best,
> Jerome
>
>
> ----- Original Message -----
> > thanks again Jerome. Sorry my question was kind of hidden .
> > Just to be clear,
> > If I submit FEP calculations straight from the dual topology file, it
> > wasn't running. So when I submitted the short run (~ 3ns) and then did
> FEP
> > calculations it worked.
> > So, 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. I wasn't sure if this part (short run with all
> > atoms(appearing & disappearing ) before FEP ) is correct or not?
> >
> > thanks,
> > Shyno
> >
> >
> > On Tue, Oct 15, 2013 at 12:29 PM, Jrme Hnin <jerome.henin_at_ibpc.fr>
> wrote:
> >
> > > 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, Jrme Hnin <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, 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
> > > > > >
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > 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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