OK, then I will switch back to CPU+sander.
Is there a tutorial for running FEP simulations? I am going through the
manual but FEP simulation is a little tricky for me as I have never done
before and I don't wanna do anything wrong.
Thanks,
Nihal
On Sun, Oct 9, 2011 at 8:14 PM, Jason Swails <jason.swails.gmail.com> wrote:
> No it does not. The capabilities of pmemd.cuda are spelled out on
> ambermd.org/gpus
>
> HTH,
> Jason
>
> On Sun, Oct 9, 2011 at 6:35 PM, E. Nihal Korkmaz <enihalkorkmaz.gmail.com
> >wrote:
>
> > Dear all,
> >
> > For FEP calculations, does pmemd.cuda work? I wanna use GPUs to do TI
> > calculations.
> > I tried but got the following error, using the input parameters I am
> > copying
> > below. I couldn't figure out what i am missing.
> >
> > Thanks,
> > Nihal
> >
> >
> > | ERROR: icfe must == 0!
> > | PMEMD 10 does not support free energies via thermo integration
> > calcs!
> > | Please use sander 10 instead.
> > | ERROR: clambda is only used if icfe != 0!
> >
> > Input errors occurred. Terminating execution.
> >
> >
> >
> > &cntrl
> > imin=0,
> > ntb=0,
> > ntx=5,
> > irest=1,
> > ntpr=200,
> > ntwr=200,
> > ntwx=200,
> > ntwe=200,
> > nstlim=500000,
> > dt=0.002,
> > icfe=1,
> > clambda=0.21132,
> > klambda=1,
> > ntt=3,
> > temp0=283.15,
> > tempi=283.15,
> > ig=-1,
> > tautp=1,
> > gamma_ln=20,
> > ntp=0,
> > pres0=1,
> > taup=1,
> > ntc=2,
> > tol=0.00001,
> > ntf=2,
> > ntb=0,
> > dielc=1,
> > cut=9999,
> > rgbmax=12,
> > ipol=0,
> > ifqnt=0,
> > igb=5,
> > saltcon=0.20,
> > rgbmax=12,
> > ioutfm=1,
> > nscm=100,
> > &end
> >
> >
> > --
> > Elif Nihal Korkmaz
> >
> > Research Assistant
> > University of Wisconsin - Biophysics
> > Member of Qiang Cui & Thomas Record Labs
> > 1101 University Ave, Rm. 8359
> > Madison, WI 53706
> > Phone: 608-265-3644
> > Email: korkmaz.wisc.edu
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644
Email: korkmaz.wisc.edu
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Received on Sun Oct 09 2011 - 19:30:03 PDT
