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 Tue Nov 24 2020 - 05:00:02 PST
