On Wed, Sep 19, 2012 at 4:57 PM, Larry Olson <nmrguy600.gmail.com> wrote:
> Im trying to refine an nmr structure using our new GPU/pmemd.cuda.
>
> I just brought over all the input files i used for sander which is
>
> simulated annealing protocol, 30
> ps
>
>
> &cntrl
>
> nstlim=30000, pencut=-0.01,
> nmropt=1,
> ntpr=200, ntt=1,
> ntwx=200,
> cut=999.0, ntb=0,
> rgbmax=16,
> igb=1,
> saltcon=0.2,
> /
>
> &ewald
>
> /
>
> #
>
> #Simple simulated annealing
> algorithm:
> #
>
> #from steps 0 to 5000: heat the system to
> 600K
> #from steps 5001-18000: re-cool to low temperatures with long
> tautp
> #from steps 18001-20000: final cooling with short
> tautp
> #
>
> &wt type='TEMP0',
> istep1=0,istep2=3000,value1=10.0,
> value2=1000.,
> /
> &wt type='TEMP0', istep1=3001, istep2=8000,
> value1=1000.0,
> value2=1000.0,
> /
> &wt type='TEMP0', istep1=8001, istep2=30000,
> value1=0.0,
> value2=0.0,
> /
>
>
> &wt type='TAUTP',
> istep1=0,istep2=8000,value1=0.2,
> value2=0.2,
> /
> &wt type='TAUTP',
> istep1=8001,istep2=24000,value1=4.0,
> value2=2.0,
> /
> &wt type='TAUTP',
> istep1=24001,istep2=27000,value1=1.0,
> value2=1.0,
> /
> &wt type='TAUTP',
> istep1=27001,istep2=29000,value1=0.5,
> value2=0.5,
> /
> &wt type='TAUTP',
> istep1=29001,istep2=30000,value1=0.05,
> value2=0.05,
> /
>
>
> &wt type='REST',
> istep1=0,istep2=8000,value1=0.1,
> value2=1.00,
> /
> &wt type='REST',
> istep1=8001,istep2=30000,value1=1.00,
> value2=1.00,
> /
>
>
> &wt type='END'
> /
> LISTOUT=POUT
>
> DISANG=RST
>
>
> Upon submission i get STOP PMEMD Terminated Abnormally!
>
>
> Looking at the output i get the following error.
> Implicit solvent radii are modified Bondi radii
> (mbondi)
> CUDA (GPU): Implementation does not currently support the use of COM
> simulations.
> Require iat(2) >= 0.
>
Did you try to define a restraint using the center of mass of a group of
atoms? (e.g., iat=-1,-1 and then setting igr1 and igr2 to groups of atoms?)
This is not allowed in pmemd.cuda after bugfix.9. Just use pmemd instead.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 19 2012 - 14:30:02 PDT
