Re: question about setting up FEP calculations

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Fri Oct 18 2013 - 11:44:41 CDT

Thanks again Jerome. I did try time steps 0.5, 0.25 still the same error
persists.
Please bear with me as I explain what I did:

1. Changed time step to 0.5
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.
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html

2. So I changed the pairlistdist, cutoff as follows:
time step =0.5, margin =3
switchdist 15.0
cutoff 16.0
pairlistdist 17.5
Reason: FATAL ERROR: Periodic cell has become too small for original patch
grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

3. increased margin upto 6, not sure if this makes sense
Then I increased margin, but still there is an error
Charm++ fatal error:
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

4. Description of the system: Disappearing atom is Hydrogen attached to a
carbon atom. Then a methyl group (connected to the previous carbon atom )
appears. In the initial file where I have all the appearing and
disappearing atoms, the appearing atoms (methyl group) apppears to be very
far from the carbon atom it is connected. I am thinking of minimizing this
initial set up first and then submitting the FEP calculation?

thanks,
Shyno

On Fri, Oct 18, 2013 at 5:33 AM, Jrme Hnin <jerome.henin_at_ibpc.fr> wrote:

> 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, 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
> >
>

-- 
Shyno Mathew
PhD student
Department of Chemical Engineering
Columbia University

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