[AMBER] Problem with heating the system

From: ATUL KUMAR <atul44_sit.jnu.ac.in>
Date: Wed, 24 Apr 2019 14:27:34 +0530

Dear amber users, I am trying to heat up a system at NVT to 50K by putting
a weak restrain on solute and the following is my input file:

Heating: heating system at NVP upto 50K
 &cntrl
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10.0,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 0.0,
  temp0 = 50.0,
  ntt = 3,
  gamma_ln = 1.0,
  nstlim = 2500, dt = 0.002,
  ntpr = 250, ntwx = 250, ntwr = 100
 /
Keep DNA fixed with weak restraints
60.0
RES 1 1487
END
END

when I run the command
pmemd.cuda -O -i heat.in -o heat.out -p md.prmtop -c min1.rst -r heat1.rst
-x heat1.nc -ref min1.rst > heat1.log &

the job is getting killed instantaneously with the following information in
the log file

cudaMalloc GpuBuffer::Allocate failed out of memory


Please help me resolve this problem.

thanks and regards
--
*Atul Kumar Jaiswal*
Research Scholar
School of Computational and Integrative Sciences
Centre for Computational Biology and Bioinformatics (CCBB)
JNU, New Delhi
India.
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Received on Wed Apr 24 2019 - 02:00:02 PDT
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