On Fri, 2014-05-30 at 15:04 +0300, Kshatresh Dutta Dubey wrote:
> Dear All,
>
> I am using Amber 14, pmemd.cuda, on Tesla K40 GPU machine. When I am
> restarting simulation from last restart file it is showing ERROR: I
> could not understand line 38756
> -0.2843673 -0.0775515 -0.0574985 1.3164001 0.0929580 1.4407944..
>
> I think that it is due to some problem in last restart file saved by
> pmemd.cuda. I want to restart the simulation from last coordinate. I have
> used ptraj to generate restart file from mdcrd file, but it does not
> contain velocity information hence I am unable to restart the simulation.
> If I am using irest=0, will new simulation represent a real restart of
> simulation from last snapshot?
Define "real restart". If you set the initial velocities to some M-B
distribution (set tempi to the same value as temp0), you can resume your
calculation. (The Andersen thermostat -- ntt=2 -- effectively does this
every vrand steps.)
If you are doing an NVE calculation looking at temporal properties (like
diffusion), then you are probably out of luck.
For future reference, I would suggest using NetCDF restart files (ntxo=2
in the input file), since there is a much lower chance of getting a
corrupted file.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 30 2014 - 06:00:03 PDT
