On Mon, Oct 18, 2010 at 3:12 AM, Ashutosh Shandilya
<izerokelvin.gmail.com>wrote:
> Hi all
> I am trying to run simulation on Tesla C2070 cuda machines (Amber11).I
> gives
> the output as STOP PMEMD terminated abnormally! and the out file says could
> not read velocities from crd file.
> My input file is
> &cntrl
> imin = 0,
> irest = 1,
> ntx=5,
>
You are specifying a restart trajectory, which requires that the inpcrd file
that you specify on the command line has velocities as well as coordinates,
so you have to check that it does. This is simple enough just by looking at
the number of lines in your crd file. Each row has 6 coordinates, which
specifies 2 atoms, so all you have to do is look at the number of lines in
your restart file (keep in mind that there is a header line, I think). If
it's not a corrupted restart file that was partially-printed during an
aborted run, then you'll have to change irest=1 and ntx=5 to irest=0 and
ntx=1.
Good luck!
Jason
> ntb=2,
> ntp = 1,
> taup=2.0,
> cut = 10,
> ntc = 2,
> ntf = 2,
> tempi = 300,
> temp0 = 300,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim =10000000, dt = 0.001,
> ntpr =10000, ntwx = 10000, ntwr = 10000
> /
> Kindly have a look.
> regards
> Shandilya Ashutosh
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Oct 18 2010 - 05:00:03 PDT
