From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Sat Nov 02 2013 - 04:24:49 CDT
Well, something is off with either your starting coordinates or the topology. It's hard to say anything more precise based on what you said.
What I'd do now is run a long minimization (say at least 10K steps) and inspect the minimization trajectory carefully in VMD.
Cheers,
Jerome
----- Original Message -----
> Hey Jerome,
> I realized the co-ordinates of the appearing atoms I was using (for the
> previous discussions) were very far off. So I wrote a new script and made
> the initial files which has all atoms (appearing, disappearing and the
> unchanging ones).
> Again, I am getting similar errors as before. Also, I did use alchemify on
> the initial files.
> I changed the time step from 1 fs to 0.003 fs. Also tried playing with the
> cutoff, pairlist dist.
> Finally time step =0.003 fs seems to work (before it wasn't passing the
> minimization stage)
> After 3100 steps, I am getting the error:
> FATAL ERROR: Low global exclusion count! System unstable or pairlistdist
> or cutoff too small.
>
> I am attaching the output file, if that helps.
>
> Following are the info in my .conf file:
> readexclusions no
> exclude scaled1-4
> 1-4scaling 0.833333333
> scnb 2.0
> temperature $temperature
>
> # OUTPUT FREQUENCIES
>
> outputenergies 100
> outputtiming 100
> outputpressure 100
> restartfreq 100
> XSTFreq 100
>
>
> # OUTPUT AND RESTART
>
> outputname 06collab
> restartname 06collab
>
> binaryoutput yes
> binaryrestart yes
>
> # CONSTANT-T
> langevin on
> langevinTemp $temperature
> langevinDamping 5.0
>
> langevinHydrogen off
>
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 124.16300010681152 0. 0.
> cellBasisVector2 0. 82.71599864959717 0.
> cellBasisVector3 0. 0. 128.3490011692047
> cellOrigin -20.06950092315674 -22.470999240875244 46.29550063610077
>
>
> # PME
> PME yes
> PMEGridSizeX 128
> PMEGridSizeY 96
> PMEGridSizeZ 160
>
> # WRAP WATER FOR OUTPUT
>
> wrapAll on
>
> # CONSTANT-P
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
>
>
> #StrainRate 0.0 0.0 0.0
> useGroupPressure yes
>
> useFlexibleCell no
> useConstantArea no
>
> # SPACE PARTITIONING
> stepspercycle 10
> margin 3.0
>
> # CUT-OFFS
>
> switching on
> switchdist 10.0
> cutoff 12.0
> pairlistdist 13.5
>
>
> # RESPA PROPAGATOR
>
> timestep 0.003
> fullElectFrequency 2
> nonbondedFreq 1
>
>
> # SHAKE
>
> rigidbonds all
>
>
>
> # FEP PARAMETERS
>
>
> alch on
> alchType FEP
> alchFile 05collab_wet.fep
> alchCol B
> alchOutFile 06collab.fepout
> alchOutFreq 100
> alchVdwLambdaEnd 1.0
> alchElecLambdaStart 0.5
> alchVdWShiftCoeff 5.0
> alchDecouple off
> alchEquilSteps 2000
>
> set Lambda0 0.0
> set dLambda 0.05
> while {$Lambda0 < 1.0} {
> alchLambda $Lambda0
> set Lambda0 [expr \$Lambda0 + \$dLambda]
> alchLambda2 $Lambda0
> run 2500
> }
>
>
>
> thanks again,
> Shyno
>
>
>
> On Fri, Oct 18, 2013 at 12:44 PM, Shyno Mathew <sm3334_at_columbia.edu> wrote:
>
> > 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, Jérôme Hénin <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, 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------=_Part_1068357_926251952.1383384289793--
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