AMBER Archive (2007)

Subject: Re: AMBER: issues with restrt file

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Jan 18 2007 - 11:07:35 CST

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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