sorry but I don't really follow what you're seeing. When you mention the
volume, do you mean the volume reported in the mdout? Or is it from
visualizing? Did you image the system?
something sounds wrong with the wallclock time requirement, are the
energies ok? if it seems ok I'm not sure why it would be so slow, could it
be a GPU problem (temperature, multiple jobs, etc)?
On Wed, Nov 25, 2020 at 12:16 PM Amit Sharma (Asstt. Prof., MCARS) <
asharma4.jmi.ac.in> wrote:
> Dear Carlos,
>
> Thanks for suggesting Dan Roe's protocol. I will try that. But, for now I
> equilibrated the dark state system (2v1a) exactly as per the method
> described in your paper. What I find is, water and ions still move a quite
> away from the protein during equilibration and the overall system has
> expanded a lot in volume. Although the production MD seems to be going
> fine, the issue now is that a 4ns simulation ( nstlim = 1000000, dt =
> 0.004) is running for about 20 mins on the GPU. Whereas, the light state
> system with the same size (2v1b, in which the system didn't expand much
> during equilibration) took only 2 mins for a 4ns production run.
>
> Kindly let me know if this expansion (and the corresponding slow down) is a
> usual thing to happen with the dark system. If not, can you please suggest
> what measures I might have missed which make my run slower.
>
> Thanks,
>
> Amit
>
>
> On Wed, Nov 25, 2020 at 8:50 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > agreed - this the one I meant earlier in the thread when I said " Dan Roe
> > also has a nice paper on equilibration"
> >
> > On Wed, Nov 25, 2020 at 10:12 AM Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > You may also want to try the system preparation protocol outlined
> > > here: https://aip.scitation.org/doi/abs/10.1063/5.0013849
> > >
> > > -Dan
> > >
> > > On Tue, Nov 24, 2020 at 7:41 AM Carlos Simmerling
> > > <carlos.simmerling.gmail.com> wrote:
> > > >
> > > > it's quite different equilibration from what we used. I don't know if
> > the
> > > > problems you are seeing are due to that, but since the 2v1b works and
> > > 2v1a
> > > > does not, it suggests that it might be due to equilibration. When
> using
> > > > 2v1a as the initial structure, you are far from equilibrium at the
> > start
> > > > and need to slowly adjust to introducing the new bond and adjusting
> to
> > > new
> > > > geometries in the flavin, etc. In my experience the GPU code can run
> > into
> > > > trouble if the system is at all unstable. You might try tracking your
> > > > energies and other properties from the mdout files and see if they
> have
> > > > reached a plateau before going to the next step, your MD stages are
> > > fairly
> > > > short.
> > > > Here is what we used that worked well for us:
> > > >
> > > > Minimization and equilibration were carried out using Amber version
> > > > 16.(39,40) Initial minimization was performed for 100 000 steps with
> > > > restraints on all atoms except hydrogens, water, C450, and the
> flavin.
> > > The
> > > > restraint force constant was 100 kcal·mol–1·Å–2. Next, the system was
> > > > heated from 100 to 298 K over 1 ns in the NVT ensemble, with a time
> > step
> > > of
> > > > 1 fs and SHAKE on all bonds including hydrogen. A nonbonded cutoff of
> > 8 Å
> > > > was used, with long-range electrostatics included by the particle
> mesh
> > > > Ewald method.(41) The same restraints were maintained. Temperature
> was
> > > > maintained using a Langevin thermostat with γ set to 1.0. Next,
> > pressure
> > > > and density were relaxed using 1 ns NPT simulation at 298 K with a
> > strong
> > > > pressure coupling constant of 0.1 and all other parameters maintained
> > > from
> > > > the prior step. Next, 1 ns MD was performed using the same protocol
> but
> > > > with restraint force constant reduced to 10.0 and pressure coupling
> > > > constant increased to 0.5. Next, minimization was performed for 10000
> > > steps
> > > > after removing all restraints except those on protein backbone CA, N,
> > > and C
> > > > atoms, and no restraints on C450. Next, 1 ns MD in the NPT ensemble
> at
> > > 298
> > > > K was performed using the same protocol as above, with restraints
> only
> > on
> > > > backbone CA, N, and C atoms excepting C450. The restraint force
> > constant
> > > > was then reduced from 10.0 to 1.0 and an additional 1 ns MD was
> carried
> > > > out, followed by 1 ns MD with restraint force constant reduced to
> 0.1.
> > > > Finally, 1 ns of fully unrestrained MD was performed with NPT at 298
> K.
> > > >
> > > > On Tue, Nov 24, 2020 at 6:44 AM Amit Sharma (Asstt. Prof., MCARS) <
> > > > asharma4.jmi.ac.in> wrote:
> > > >
> > > > > I tried simulation using 2v1b (crystal structure in photoexcited
> > > state). It
> > > > > works fine in that case and is currently running at 2 micro second.
> > > > >
> > > > > My equilibration protocol is as follows
> > > > >
> > > > > 1. 3000 cycle minimization under 100 kcal mol-1 A-2 restraint on
> the
> > > > > protein
> > > > > 2. 5000 cycle minimization under 25 kcal mol-1 A-2 restraint on the
> > > protein
> > > > > 3. 100000 cycle minimization without any restraints
> > > > > 4. 20ps md at nvt where system was heated from 0 to 300K, with 10
> > kcal
> > > > > mol-1 A-2 restraint on the protein, 2fs time step by keeping SHAKE
> > on.
> > > cut
> > > > > of 10 A
> > > > > 5. 80ps md at nvt at 300 K, with 0.5 kcal mol-1 A-2 restraint on
> the
> > > > > protein, 2fs time step by keeping SHAKE on. cut of 10 A
> > > > >
> > > > > System remains fine until step 5, but blows when I start (using
> gpu)
> > > ntp
> > > > > (ntb = 2, pressure 1atm, ntp = 1) at 300K.
> > > > >
> > > > >
> > > > > When doing the same using cpu, it seems fine at least for initial
> > > 100ps.
> > > > > But, issue is that I cannot go on cpu for the simulation where a
> few
> > > micro
> > > > > second run is needed before we could actually see J alpha
> unfolding.
> > > > >
> > > > > In your paper you retain the crystallographic water and use four
> > point
> > > opc
> > > > > water. But, what I am using is tip3p. Can that make a difference?
> > > > >
> > > > > Amit
> > > > >
> > > > >
> > > > > On Tue, Nov 24, 2020 at 4:40 PM Carlos Simmerling <
> > > > > carlos.simmerling.gmail.com> wrote:
> > > > >
> > > > > > Have you tried the simulation without adding the adduct? Also you
> > > didn't
> > > > > > describe your equilibration protocol. I believe the one we used
> > > should be
> > > > > > described in our paper on that system. Dan Roe also has a nice
> > paper
> > > on
> > > > > > equilibration.
> > > > > > Carlos
> > > > > >
> > > > > > On Tue, Nov 24, 2020, 6:05 AM Amit Sharma (Asstt. Prof., MCARS) <
> > > > > > asharma4.jmi.ac.in> wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > I trying to simulate protein having of FMN Cys adduct.
> > > > > > >
> > > > > > > When running md using nvt and positional restraints of 0.5 kcal
> > > mol-1
> > > > > A-2
> > > > > > > on the protein, the system remains fine.
> > > > > > >
> > > > > > > But as I switch to npt and remove all the restraints system
> blows
> > > up
> > > > > and
> > > > > > > water molecules start flying away.
> > > > > > >
> > > > > > > Error message is as follows:
> > > > > > >
> > > > > > > "ERROR: Calculation halted. Periodic box dimensions have
> changed
> > > too
> > > > > > much
> > > > > > > from their initial values.
> > > > > > > Your system density has likely changed by a large amount,
> > > probably
> > > > > from
> > > > > > > starting the simulation from a structure a long way from
> > > equilibrium.
> > > > > > >
> > > > > > > [Although this error can also occur if the simulation has
> blown
> > > up
> > > > > for
> > > > > > > some reason]
> > > > > > >
> > > > > > > The GPU code does not automatically reorganize grid cells and
> > > thus
> > > > > you
> > > > > > > will need to restart the calculation from the previous
> restart
> > > file.
> > > > > > > This will generate new grid cells and allow the calculation
> to
> > > > > > continue.
> > > > > > > It may be necessary to repeat this restarting multiple times
> if
> > > your
> > > > > > > system
> > > > > > > is a long way from an equilibrated density.
> > > > > > >
> > > > > > > Alternatively you can run with the CPU code until the density
> > has
> > > > > > > converged
> > > > > > > and then switch back to the GPU code."
> > > > > > >
> > > > > > > Can anyone suggest how to deal with this?
> > > > > > >
> > > > > > > Thank You,
> > > > > > >
> > > > > > > Amit
> > > > > > >
> > > > > > > --
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Received on Wed Nov 25 2020 - 09:30:03 PST
