Re: [AMBER] Need help for retrained MD (Daniel Roe)

From: Sudhanshu Shanker <>
Date: Fri, 17 Oct 2014 12:50:40 +0530

Hello All,

Thanks Jason and Daniel for your suggestions, I tried the "distance_COM"
example and it worked for me (for pmemd ), but when I am using
'pmemd.cuda' for the submission of job, It prompts the message "*STOP
PMEMD Terminated Abnormally! *" with "*CUDA (GPU): Implementation does
not currently support the use of COM simulations. Require iat(2) >= 0*."
in output file.

In my work I am trying to calculate PMF of the system using different
positions of ions, and I need to use CUDA for this purpose. If I know a
point in space, where i need to apply restrain from, can I use the
coordinates of this point without using COM type simulation to make it work
for 'pmemd.cuda' or is there any other possible way to use this type of
restrain for CUDA.

Input file:

  nstlim= 25000000, dt=0.002, ntx=5, irest=1,
  ntpr=500, ntwr=500, ntwx=500,
  temp0=300.0, ntt=1, tautp=2.0, ig= -1,
  ntb=2, ntp=1,
  ntc=2, ntf=2,
 &wt type='DUMPFREQ', istep1=2
 &wt type='END'

  r1=2.72, r2=7.72, r3=7.72, r4=12.72,
  rk2 = 10.0, rk3 = 10.0,
  igr1=0,0,0,0, igr2=195,196,511,517,

Thanks in advance,

- Sudhanshu

*Sudhanshu Shanker      *
*Center for Computational Biology and BioinformaticsSchool of Computational
and Integrative SciencesJawaharlal Nehru UniversityNew Delhi-110067INDIA
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Received on Fri Oct 17 2014 - 00:30:02 PDT
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