Gerald, the molecules are the ones in the amber ionic liquid tutorial, so
bigger than water. I just tried to set skinnb = 4.0 under &ewald in my
input script, and am getting basically the same behavior as with the
default skinnb (total energy vs time stays roughly flat for ~ 1 ns or so,
and then starts to really shoot up, giving an overall drift of about 6 x
10^-4 kT/ns/dof).
Jason, I was not using SHAKE in the 1 fs timestep runs, however in the 2 fs
runs I did. I have two runs (that started from different annealing
protocols, so this is not really comparing apples to apples I suppose) and
those used the following parameters
dt = 0.002
ntc=ntf=2
And default values for tol and dsum_tol
Results in drift = 1.0 x 10^-2 kT/ns/dof
dt = 0.002
ntc=ntf=2
tol = 0.000001
dsum_tol = 0.000001
Results in drift = 2.6 x 10^-3 kT/ns/dof
This makes it appear that there is almost an order of magnitude improvement
in the drift when those tolerance values are changed, however, the second
case was the result of a longer (and probably better) annealing scheme. If
you don't think that this is telling, I can run a more controlled test of
the tolerance parameter by using the same starting configuration in each
case. Is it worth is to make the tolerance even smaller than 10^-6?
Thanks for the help.
Joe
On Thu, Jan 22, 2015 at 3:05 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> Are you SHAKEing bonds with Hydrogen? If so, did you look at the effect
> that the SHAKE tolerance had on energy conservation? A big difference
> between an IL and water with respect to constraint solving is that water
> constraints can be solved analytically (so you shouldn't see any kind of
> energy drift coming from water regardless of what the SHAKE tolerance is, I
> think).
>
> If the solvent becomes mostly molecules with more than 3 points and
> restraints, you can't solve their constraint equations using SETTLE and
> have to fall back to the iterative SHAKE algo (and hence, the tolerance
> becomes more important). This would explain why the drift is larger with
> IL than with water-and-protein (unless I'm missing something).
>
> HTH,
> Jason
>
> On Thu, Jan 22, 2015 at 2:20 PM, Joseph Baker <bakerj.tcnj.edu> wrote:
>
> > This didn't go through the first time because I wasn't subscribed yet.
> > Ross, some answers to your questions below. Thanks!
> >
> > On Thu, Jan 22, 2015 at 1:48 PM, Ross Walker <ross.rosswalker.co.uk>
> > wrote:
> >
> > > Hi Joe,
> > >
> > > I've moving this over to the AMBER mailing list as I think this is of
> > > interest to others and they maybe able to offer more suggestions than
> me.
> > >
> > > My initial guess is that this may be due to the way PME is working with
> > > ionic liquids. Are the systems definitely neutral in all cases? The
> > > behavior of PME maybe different if the system is not neutral.
> > >
> > >
> > In the amber output files the "sum of charges" line says that
> > Sum of charges from parm topology file = -0.00020404 (pure IL
> system)
> > Sum of charges from parm topology file = -0.00102021 (waters +
> > IL)
> > So they look to be effectively charge neutral.
> >
> >
> > > My second suspicion is that the average velocities might be higher for
> > > ionic liquids - have you tried at different temperatures.
> > >
> >
> > I have not tried at different temperatures. One of the preparation
> > protocols tried was that the system was annealed up to 500 K and then
> > brought back down to 300 K (in NPT using langevin thermostat and monte
> > carlo barostat). Then left to run at 300 K in NPT for a bit before
> > switching to NVE simulations.
> >
> >
> > > In the case of a protein in TIP3P water with Shake you have no atoms
> that
> > > are affectively unconnected to anything else. So your waters have an
> > > effective mass of 18 per molecule and your protein has a huge per
> > molecule
> > > mass. The waters are less than sodium for example in mass but there may
> > be
> > > hydrogen bonding effects, or their VDW are different such that they are
> > > moving less. This is just a stream of conciousness - I am not sure why
> > > you'd see the difference but I could image there being more effective
> > loss
> > > of precision somewhere due to either - charge charge interaction being
> > > larger on average - bigger +'ve and -'ve numbers that cancel out for
> > > example. This sort of thing would certainly effect energy conservation
> > > within the SPFP precision model.
> > >
> > > There might also be more integration error going on if the particles
> are
> > > moving faster although that would imply a higher overall temperature.
> > Does
> > > reducing the timestep help?
> > >
> > >
> > So, this is a series of runs that were done of a pure IL system (the one
> > from the Amber tutorial with just gaff charges) with 3984 atoms in NVE
> > starting from the end of just a short annealing protocol, and the
> timestep
> > was changed to see the influence
> >
> > dt = 0.0001
> > drift = 1.8 x 10^-4 kT/ns/dof
> >
> > dt = 0.005
> > drift = 2.9 x 10^-4 kT/ns/dof
> >
> > dt = 0.001
> > drift = 3.6 x 10^-4 kT/ns/dof
> >
> > dt = 0.002 (with ntc=ntf=2)
> > drift = 1.0 x 10^-2 kT/ns/dof
> >
> > To get these drifts I just did a simple linear regression through the
> > entire NVE Etot vs time dataset using xmgrace.
> >
> > (I can give more details on how each of these were run if it is useful at
> > some point)
> >
> > I also tried to check the energy drift for another ammonium salt system
> (in
> > water, 20917 atom system) that my collaborator I'm working on these ILs
> > with had from some previous work, and there the drift in NVE looked much
> > better
> >
> > dt = 0.001
> > drift = -2.0 x 10^-5 kT/ns/dof
> >
> > He did not just use gaff for the ammonium salt charges, so could this
> just
> > be an issue of needing to do a more refined charge fitting?
> >
> >
> > > Have you tried DPFP to see how it does with that?
> > >
> >
> > I did try DPFP at a 2 fs step (same as the pure IL system described
> above),
> > and there I got
> >
> > dt = 0.002
> > ntc=ntf=2
> > drift = 8.8 x 10^-3 kT/ns/dof
> >
> > So it was a little better than the 2 fs timestep in SPFP
> >
> >
> > >
> > > Anyone else want to chime in?
> > >
> > > All the best
> > > Ross
> > >
> > >
> > Thanks for the input.
> >
> > Joe
> >
> > > On Jan 20, 2015, at 3:26 PM, Joseph Baker <bakerj.tcnj.edu> wrote:
> > >
> > > Hi Ross,
> > >
> > > I hope you've been doing well. I've got a question for you in relation
> to
> > > trying to compare some energy drifts to your paper on explicit solvent
> > PME
> > > in GPU amber. My protein simulations have NVE drift that is spot on (5
> x
> > > 10^-6 kT/ns/dof for 1 fs steps, and 1.3 x 10^-5 kT/ns/dof for 2 fs
> step),
> > > so that's been very nice (the code really does great for energy
> > > conservation in the protein NVE sims).
> > >
> > > However, I've tried to dabble a bit with some ionic liquids (currently
> am
> > > testing the one that is in the amber ionic liquid tutorial that uses
> gaff
> > > parameters). There I've tried a whole ton of different timestep,
> cutoff,
> > > equilibration protocol combinations, and the best I can seem to get is
> > > around a couple x 10^-4 kT/ns/dof (these are pure ionic liquid
> > simulations,
> > > but I get a similar result in a simulation where I sprinkled the ionic
> > > liquid inside a box of water, actually there I get a bit worse, about
> > 10^-3
> > > kT/ns/dof). I realize that this is still not very large at all, but do
> > you
> > > have any reason to believe that pmemd.cuda with ionic liquids is going
> to
> > > do worse in NVE?
> > >
> > > If you've got a spare minute at some point for an opinion on this, it
> > > would be appreciated!
> > >
> > > Thanks,
> > > Joe
> > >
> > > --
> > > Joseph Baker, PhD
> > > Assistant Professor
> > > Department of Chemistry
> > > C101 Science Complex
> > > The College of New Jersey
> > > Ewing, NJ 08628
> > > Phone:(609) 771-3173
> > > Web:http://bakerj.pages.tcnj.edu/
> > > <https://sites.google.com/site/bakercompchemlab/>
> > >
> > >
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jan 22 2015 - 13:00:02 PST
