AMBER Archive (2003)

Subject: Simple question about sander parameter set

From: Peng Tao (ptao_at_chemistry.ohio-state.edu)
Date: Tue May 13 2003 - 09:44:40 CDT

Dear AMBER users,

I am trying to use AMBER to do a simple protein MD. When I used NRUN
parameter, no matter how long I run sander ( about 100 hours on 8 nodes
with 2 cpus on each node), I never got any output. The size of .out file
is zero, and no other output file exists in running directory.
The whole .in file is like
/////////////////////////////////
1d7a MD run
 &cntrl
    imin=0, irest=0, ntx=1, tempi=0.,
    ntt=1, temp0=300.0, tautp=0.2,
    ntp=2, taup=0.2,
    ntb=2, ntc=2, ntf=2,
    nrun=2 ,nstlim=500,
    ntwe=100, ntwx=100, ntpr=25,
 &end
///////////////////////////////////

When I discarded nrun parameter, and set nstlim as the product of the
previous nrun and nstlim, I got normal output: .out and .info files
updated every 25 steps, and .restrt and .traj updated frequently ( not
sure how often). The whole simulation can be done in 20 minuets.
The whole .in file is listed below.
////////////////////////////////////////
1d7a MD run
 &cntrl
    imin=0, irest=0, ntx=1, tempi=0.,
    ntt=1, temp0=300.0, tautp=0.2,
    ntp=2, taup=0.2,
    ntb=2, ntc=2, ntf=2,
    nstlim=1000,
    ntwe=100, ntwx=100, ntpr=25,
 &end
///////////////////////////////////////

I know there must something wrong with the combination I used with nrun,
but I couldn't figure out what it is.

Thank you for your help on this naive problem.

Best regards,
Peng Tao