I'm not sure, it could be file system problems or
other things, but you might want to try writing the
restart more often (ntwr of 500 or so).
Try re-running and see if it is reproducible or not.
Amit Kumar wrote:
> Hello Amber users,
>
> I am doing simulations is parallel using sander.MPI command in Amber9.
> I did 1 ns simulation. The output file (md.out) shows that the 1 ns
> simulation was completed
> successfully. But when I opened the restrt file and it shows the
> co-ordinate for 860 ps instead of 1000 ps. And when I restart the
> simulation it starts at 860 ps instead of 1ns, but the mdout file
> shows the simulation went on well till 1ns. I am not sure why my
> restrt file doesn`t have final crd for 1000ps. My input file for the
> MD simulation was
>
> MD Generalise Born, no cut off
> &cntrl
> imin = 0, ntb = 0,
> igb = 5, ntpr = 100, ntwx = 1000,
> ntt = 3, gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0,
> nstlim = 500000, dt = 0.002,
> cut = 999, ntwr = 10000,
> /
>
> I will appreciate your comments.
>
> Amit
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Received on Sun Jan 21 2007 - 06:07:23 PST
