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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>
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Received on Tue Feb 12 2019 - 06:30:03 PST
