[AMBER] amber pmemd.cuda for implicit solvent simulations

From: Prithviraj Nandigrami <prithviraj.nandigrami.einsteinmed.edu>
Date: Wed, 15 Dec 2021 19:45:11 +0000

Dear All,

I am using AMBER's implementation of pmemd.cuda to run an implicit solvent simulation. My input file is below:


minimization 01 - implicit solvent
 &cntrl
  imin = 1, maxcyc = 1000, ncyc = 100,
  ntx = 1, ntc = 1, ntf = 1,
  ntb = 0, ntp = 0, ntxo = 1, ioutfm = 0,
  ntwx = 100, ntwe = 0, ntpr = 100,
  igb = 1, cut = 9999.0,
  ntr = 1, restraintmask = ':1-X_LASTREC_RESIDNO_X & !.H= | :X_LIG_RESIDNO_X.CG', restraint_wt=5.0,
/

The executable I am using to run this input file is: pmemd.cuda

However, the simulation fails with the following error message:


Note: ig = -1. Setting random seed to 676892 based on wallclock time in
      microseconds.
| irandom = 1, using AMBER's internal random number generator (default).
CUDA (GPU): Implementation does not support the use of a cutoff in GB simulations.
            Require cut > 999.0d0.

 Input errors occurred. Terminating execution.


I do not know what is causing this error as the cut value set in my input file is > 999.0d0 (as required for GB simulations). Any help would be much appreciated.


Thank you.
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Received on Wed Dec 15 2021 - 12:00:03 PST
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