I am pretty sure that there is no way to do FEP calculations in amber at
this moment.
I believe you mean free energy calculations and NOT FEP (which stands
for free energy perturbation, a METHOD to compute free energies).
If so, the method implemented in amber is TI (Thermodynamic Integration,
a VERY different method than FEP).
There is a tutorial for TI, try to follow that one.
Adrian
On 10/9/11 10:15 PM, E. Nihal Korkmaz wrote:
> 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
>>
>
>
>
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Sun Oct 09 2011 - 19:30:03 PDT
