AMBER Archive (2004)

Subject: AMBER: sander gets stuck

From: MURAT CETINKAYA (cetinkayam_at_psu.edu)
Date: Fri Oct 29 2004 - 09:32:22 CDT

Hello,

I am trying to perform 1ns MD of a protein with an explicit solvent. I am
following the same procedure described in DNA tutorial and it always works.
However for this system, my output files always get stuck at 220ps and I found
the following message in my computer nodes:

FLUSH--FAILED:: Stale NFS file handle
FLUSH--FAILED:: Stale NFS file handle

Input/Output Error 173: unknown error

   In Procedure: amopen
        At Line: 78

      Statement: CLOSE
           Unit: 6
   Connected To: MD_w_step2.out
           Form: Formatted (contains List-Directed records)
         Access: Sequential
Records Read : 0
Records Written: 780

End of diagnostics

My MD input file is:
1ns MD_step2
 &cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 10.0,
  cut = 10, ntr = 0,
  tempi = 300.0, temp0 = 300.0,
  ntt = 1,
  nstlim = 1000000,
  ntpr = 5000, ntwx = 2000, ntwr = 2000
 /
I have no idea about this problem. Anybody can help me?

Thanks

Murat CETINKAYA
Biomolecular Materials Lab,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
web: www.personal.psu.edu/muc176
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu