Hi,
I found another solution for ''Periodic box dimensions have changed too
much from their initial values'' ( I don't know whether someone also have
tried it!!). I use pmemd.cuda.MPI instead of pmemd.cuda just for density
equilibration (for single GPU too) and it always works fine to me.
Therefore I bypass time consuming cpu run or multiple-time restarting
simulations which seems annoying, specially if I am using clusters in
queuing.
regards
Kshatresh
On Thu, May 24, 2018 at 2:19 PM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> I’m sorry, I did not read the complete message and missed that you’d
> already corrected for this initial error.
>
> // Gustaf
>
> > On 24 May 2018, at 14:07, Karolina Mitusińska (Markowska) <
> markowska.kar.gmail.com> wrote:
> >
> > Dear Amber Users,
> >
> > I want to run a simulation of a protein-ligand complex immersed in
> water. I
> > have a complete PDB file and I only want to generate the topology
> (.prmtop)
> > and coordinates (.inpcrd) files.
> >
> > I've tried:
> > source leaprc.ff14SB
> > loadamberparams frcmod.ionsjc_tip3p
> > loadamberparams ../TSO.frcmod
> > loadoff ../TSO.lib
> >
> > prot = loadpdb complete_pdb.pdb
> >
> > check prot
> > charge prot
> >
> > saveamberparm prot complete_pdb.prmtop complete_pdb.inpcrd
> > quit
> >
> > but then my simulation did not start and PMEMD gave me an error that say:
> > ERROR: Box parameters not found in inpcrd file!
> >
> > So I modified my tleap script
> > source leaprc.ff14SB
> > loadamberparams frcmod.ionsjc_tip3p
> > loadamberparams ../TSO.frcmod
> > loadoff ../TSO.lib
> >
> > prot = loadpdb complete_pdb.pdb
> >
> > check prot
> > charge prot
> > setbox prot vdw
> >
> > saveamberparm prot complete_pdb.prmtop complete_pdb.inpcrd
> > quit
> >
> > And now my simulation crashes during equilibration step with a longer
> error
> > message:
> > 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.
> >
> > And although I find that message quite informative, I don't know how to
> > manage with my simulation.
> >
> > I'm using pmemd.CUDA for all simulations steps, I've tried to run some of
> > them using the regular pmemd, but I'm still having the same error.
> >
> > Could this error be related with the preparation of the PDB file?
> > How should I prepare my complete PDB file?
> >
> > Many thanks for your help!
> > Karolina Mitusińska
> > PhD student
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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>
--
With best regards
************************************************************************************************
Dr. Kshatresh Dutta Dubey
Researcher,
Institute of Cell and Molecular Biology
Uppsala University
Uppsala, Sweden
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Received on Thu May 24 2018 - 06:30:04 PDT
