Dear all,
I have a problem when using distance restraint with pmemd :
Here is one of my output files :
JID OWNER COMMAND
------------------ -------------- --------------
0x783d000000000d11 cailliez /usr/local/lsf4.1/etc/res -d
/usr/local/lsf4.1/etc -m athena /home/caill
iez/.ls
LIMIT NAME USAGE HIGH USAGE CURRENT LIMIT MAX LIMIT
------------------ -------------- -------------- --------------
--------------
cputime 0 0 unlimited unlimited
datasize 976k 976k unlimited unlimited
files 14 16 8000 12000000
vmemory 6896k 6896k unlimited unlimited
ressetsize 1680k 4352k 8000000k 16g
threads 0 0 unlimited unlimited
processes 4 4 unlimited unlimited
physmem 1680k 4352k unlimited unlimited
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
Warning: Error opening "New" file from subroutine OPNMRG
File =
I already had this problem before and the bugfix.31 patch was proposed
to solve this
problem, but it seems that it does not solve the problem entirely.
As the warning is written 15 time and I work with 16 processors on
SGI Origin 3800, I guess it is due
to processors wanted to write in the same place.
This problem does not seem to affect the calculations but is still annoying.
Any help will be appreciated,
Thanks in advance,
Fabien
PS : her are my input files :
*************************************************************************
***************************** md.in *****************************
*************************************************************************
100 ps MD production at constant T= 300K & P= 1Atm and coupling = 5..0
&cntrl
imin=0, ntx=5, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
nscm=5000,
ntf=2, ntc=2,
ntb=2, ntp=1, tautp=5.0, taup=5.0,
nstlim=150000, t=0.0, dt=0.002,
cut=9.0,
ntt=1,nmropt=1,
irest=1
/
# Distance restraint
&wt type='DUMPFREQ', istep1=10, &end
&wt type='END', &end
DISANG=dist.900.in
DUMPAVE=dist900_vs_t
#
# 2 TRP CD2 37 ILE N 10
&rst
iat=36, 599, r1= 0.0, r2 = 9.0, r3 = 9.0, r4 = 999.0,
rk2=25.0, rk3=25.0, ir6=0, ialtd=0,
&end
--
__________________________________________________________________
Fabien Cailliez Tel : 01 58 41 51 63
Laboratoire de Biochimie Théorique e-mail : cailliez.ibpc.fr
IBPC 13, rue Pierre et Marie Curie
75005 Paris
__________________________________________________________________
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Received on Thu Apr 14 2005 - 14:53:00 PDT
