AMBER Archive (2005)

Subject: AMBER: pmemd and distance restraint

From: Fabien Cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Thu Jan 20 2005 - 04:39:20 CST

Dear all,

I am using pmemd to run a distance-restrained simulation on a. I have a
weird message.
I am running this simulation on 16 processors on SGI Origin 3800.
The information output is :
JID OWNER COMMAND
------------------ -------------- --------------
0x783d00000000d8a5 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 2480k 2480k unlimited unlimited
files 14 19 8000 12000000
vmemory 7440k 8224k unlimited unlimited
ressetsize 3552k 4368k 8000000k 16g
threads 0 0 unlimited unlimited
processes 4 4 unlimited unlimited
physmem 3552k 4368k 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 =

The simulation does not stop and everything seems to go well (except
this message).
There are 15 times the same repeat in the message an I am running my
simulation on 16 processors.
Can it be that all the processors want to open the same file ?
Do I need to worry about this message ?

Yours sincerely,
Fabien

My input files are :
*************************************************************************
***************************** md.in *****************************
*************************************************************************
100 ps MD production at constant T= 300K & P= 1Atm and coupling = 5.0
&cntrl
   imin=0, ntx=7, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
   nscm=500,
   ntf=2, ntc=2,
   ntb=2, ntp=1, tautp=5.0, taup=5.0,
   nstlim=50000, t=0.0, dt=0.002,
   cut=9.0,
   ntt=1,nmropt=1,
   irest=1
&end
# Distance restraint
&wt type='DUMPFREQ', istep1=10, &end
&wt type='END', &end
DISANG=dist.900.in
DUMPAVE=dist900_vs_t

and the file DISANG is :
#
# 2 TRP CD2 37 ILE N 10
&rst
 iat=36, 599, r1= 0.0, r2 = 9.0, r3 = 9.0, r4 = 999.0,
 rk2=50.0, rk3=50.0, ir6=0, ialtd=0,
&end 

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

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