Thanks ! Now its fine but there is still one error left.I used TIP3P
waterbox but it still says
Implementation does not support extra points.
Require numextra == 0
My input is
MD equilibration on protein
&cntrl
imin = 0,
irest = 0,
ntx=1,
ntb=2,
ntp = 1,
taup=2.0,
cut = 10,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 5.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 2500, dt = 0.001,
ntpr =2500, ntwx = 2500, ntwr = 5000
/
Thanks and regards
Shandilya Ashutosh
On 18 October 2010 17:03, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Oct 18 2010 - 23:30:05 PDT
