To add to the good advice you've already gotten, I like to take my entire
replica exchange simulation set up, remove numexchg and set a reasonable
nstlim, and just let it run (for like an hour or two) without exchanges to
measure the potential energy histograms at each temperature. I find it's
overall less work on my part than post-processing.
-Christina
On Wed, Aug 5, 2020 at 9:15 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Double check that you've really got the energies from MDOUT sorted by
> temperature; as Koushik said that really does look like replica space.
> Another possibility is that your temperature spacing is too small, but
> you'd still expect a more Gaussian shape if that were the case. One
> thing you could do to check would be to sort the trajectories
> themselves (with 'ensemble') and then get energies via post-processing
> the sorted trajectories (using either sander imin=5 or cpptraj
> 'energy' etc).
>
> Sorting generic replica datasets is on my to-do list for cpptraj;
> actually cpptraj will sort constant pH replica data now, just needs to
> be extended to other data sets.
>
> -Dan
>
> On Wed, Aug 5, 2020 at 8:35 AM Diego Morone <diego.morone.irb.usi.ch>
> wrote:
> >
> > Dear AMBER users,
> >
> >
> >
> > I am trying to set up replica exchange on AMBER. Using explicit solvent
> > (ff14SB + TIP3P water) and 16 geometrically spaced replicas I get a good
> > range of accept ratios (from 5 to 16 %) and 10-20 round trips/replica,
> but
> > weird histograms (see attachment) which don't look like gaussians. The
> > simulation is run for 40ns/replica on 2 GPUs with pmemd.cuda.MPI on Amber
> > 19. After heating at 300K, the equilibration was performed first NPT at
> 300K
> > 1atm, then NVT at 300K. I get a similar plot with implicit solvent and
> less
> > replicas. Could you help me in spotting the problem?
> >
> >
> >
> > Many thanks
> >
> > Diego
> >
> >
> >
> > TREMD
> >
> > &cntrl
> >
> > imin = 0,
> >
> > irest = 0,
> >
> > ntx = 1,
> >
> > ntt = 3,
> >
> > gamma_ln = 1.0,
> >
> > temp0 = TEMPERATURE,
> >
> > cut = 9.0,
> >
> > ntc = 2,
> >
> > ntf = 2,
> >
> > nstlim = 10,
> >
> > dt = 0.002,
> >
> > ig = RANDOMNUM,
> >
> > numexchg = 2000000,
> >
> > iwrap = 1,
> >
> > ntpr = 5000,
> >
> > ntwr = 5000,
> >
> > /
> >
> > &wt TYPE='END'
> >
> > /
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-----------------------------------------------------------------
Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Wed Aug 05 2020 - 07:00:03 PDT
