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
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Received on Fri Oct 29 2004 - 15:53:00 PDT
