Dear Pratul and Shayna,
Thank you very much for the answers and a very good idea.
-Chetna
On Tue, Feb 12, 2019 at 3:24 PM Shayna Hilburg <shayna.hilburg.gmail.com>
wrote:
> The setting ntwr will set how often to write the restart file. So include
> ntwr=10000 or whatever interval you'd like into your commands in the .in
> file next time.
> Seeing as it wasn't written yet though, I'm not totally sure how to help
> with the simulation you've already ran. Perhaps extract the last frame of
> the .nc file using cpptraj and then start a new simulation for the
> appropriate amount of time using those coordinates and velocities?
>
> Good luck!
>
> On Tue, Feb 12, 2019 at 6:10 AM Chetna Tyagi <cheta231.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > During accelerated MD simulations, the restart file is not formed until
> the
> > simulation has completed (all steps in the input).
> > So, in my case, the simulation stopped before completing as it ran out of
> > time at the server.
> > I can't restart from that point as no restart file is available.
> >
> > The input file,
> > vt-continue
> > &cntrl
> > imin=0,irest=1,ntx=5,
> > nstlim=500000000,dt=0.002,
> > ntc=2,ntf=2,ig=-1,
> > cut=10.0, ntb=1, ntp=0,
> > ntpr=1000, ntwx=1000,
> > ntt=3, gamma_ln=2.0,
> > temp0=300.0,ioutfm=1,iwrap=1,
> > iamd=3,
> > ethreshd=293, alphad=16,
> > ethreshp=-42929, alphap=2311,
> > /
> >
> > And my command,
> >
> > *mpirun pmemd.cuda.MPI -O -i amd.in <http://amd.in> -o amd2.out -p
> > PCI.prmtop -c Prod.rst -r amd2.rst -x amd2.nc <http://amd2.nc> -ref
> > Prod.rst -inf amd2.info <http://amd2.info>*
> >
> > What am I missing? And how can I solve this problem?
> >
> > I have not found any way to restart using the trajectory (.mdcrd or .nc
> > file) but is there any way?
> >
> > Thank you,
> >
> > --
> > Best wishes
> > Chetna
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
Best wishes
Chetna
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Received on Wed Feb 13 2019 - 03:30:02 PST
