Hi there!
How long is your heating step? Because if its too long you will have to
restart the calculation every 500ps (roughly) and increase the skinnb
value, due to changes in system density during the heating. Pmemd.cuda does
not recalculate the non bond list cells, so if they change too much due to
changes in system size, program will stop.
Hope it helps!
Gera!
El lun., 22 jun. 2020 08:22, <rosaester.forgione.unina.it> escribió:
> I want to add that after some steps of the production the same error
> appears 2/3 times and then the calculation stops :
>
> PRODUCTION
> Mon 22 Jun 2020 01:12:04 PM WEST 1 ns
> Mon 22 Jun 2020 01:15:26 PM WEST 2 ns
> Mon 22 Jun 2020 01:18:49 PM WEST 3 ns
> 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.
>
> Mon 22 Jun 2020 01:19:58 PM WEST 4 ns
> 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.
>
> Mon 22 Jun 2020 01:20:00 PM WEST 5 ns
>
> Unit 9 Error on OPEN: PRODUCTION-4.restrt
> STOP PMEMD Terminated Abnormally!
>
>
>
> Quoting rosaester.forgione.unina.it:
>
> > Hi,
> >
> > I am facing problems in running MD dynamics by using PMEMD.CUDA
> >
> > During the 300 K heating step (NPT) the following error appears:
> >
> > 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.
> >
> > However, the MD simulations goes on passing to the production steps.
> >
> > I tried to restart the simulation from the previous restart file, as
> > suggested by the error message, but it doesn't work since the same
> > error appears.
> >
> > I used the same equilibration protocol that I routinely use to
> > carry on MDs on ligands alone (glycans) and protein-ligand complex.
> >
> > I tried to run a MD simulation on an "old" system, already analyzed
> > with amber without any issue, and the same error appears. Thus, it
> > seems that the problem is not strictly related to the parameters of
> > the system.
> > I also run the simulation on GPU 0 and then on 1 and the error is
> > still there.
> >
> > Anyone can suggest how to fix this problem?
> >
> > Thanks in advance,
> >
> > Rosa
> >
> >
>
>
>
>
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Received on Mon Jun 22 2020 - 05:00:02 PDT
