Re: question about setting up FEP calculations

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Oct 18 2013 - 04:33:54 CDT

What happens if you start the MD with a 0.5 fs time step?

Jerome

----- Original Message -----
> 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, Jérôme Hénin <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, Jérôme Hénin <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, 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
> > > > >
> > > >
> > >
> > >
> > >
> > > --
> > > Shyno Mathew
> > > PhD student
> > > Department of Chemical Engineering
> > > Columbia University
> > >
> >
>
>
>
> --
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University
>

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