AMBER Archive (2009)

Subject: [AMBER] help with TIP4P and mpi pmemd

From: Hashem Taha (hashemt_at_gmail.com)
Date: Thu Dec 03 2009 - 16:16:22 CST

I have a problem with trying to run some jobs using TIP4P water as the
solvent. I have tried running the same exact files with TIP3P water and the
calculations started and completed perfectly. However, upon changing from
TIP3P to TIP4P, my calculations would stop without reason. the file that I
am trying to run is just a water minimization and it results in the
following errors. The input file is also included below. The calculations
start but after a few steps they come to a halt. Any help would be
appreciated, and if you require further information please let me know...

HT

the errors are:

>forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line
Source
pmemd 000000000048265A Unknown Unknown Unknown
pmemd 00000000004777C3 Unknown Unknown Unknown
pmemd 00000000004AA1D5 Unknown Unknown Unknown
pmemd 00000000004CA1CE Unknown Unknown Unknown
pmemd 000000000040744C Unknown Unknown Unknown
libc.so.6 0000003F4D81D8B4 Unknown Unknown Unknown
pmemd 0000000000407359 Unknown Unknown Unknown
rank 7 in job 55 compute-0-8.local_45343 caused collective abort of all
ranks
  exit status of rank 7: killed by signal 9

the input file...

Constant Volume Minimization
 # Control section
 &cntrl
  ntwx = 50, ntpr = 1, ntwr = 1,
  scnb = 1.0, scee = 1.0, nsnb = 25, dielc = 1, cut = 8.0,
  ntb = 1,
  maxcyc = 1000, ntmin = 0, dx0 = 0.01, drms = 0.0001,
  ntp = 0,
  ibelly = 0, ntr = 1,
  imin = 1,
 &end
Group Input for restrained atoms
5.0
RES 1 2
END
END
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