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 - 04:00:02 PST
