Thanx ....
I also wanted to know if it is fine to generate a crd file from the pdb file
using tleap and then restarting the simulation. Will I be losing some
information.
Amit
On 1/18/07, Carlos Simmerling <carlos.csb.sunysb.edu> wrote:
>
> 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 - 06:07:24 PST
