AMBER Archive (2007)

Subject: AMBER: issues with restrt file

From: Amit Kumar (amitkumar346_at_gmail.com)
Date: Thu Jan 18 2007 - 10:15:52 CST


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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