Hi,
On Fri, Oct 17, 2014 at 1:20 AM, Sudhanshu Shanker
<sudhanshu.bioinfo.gmail.com> wrote:
>
> 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.
Unfortunately no, as the message states you can't use center of mass
restraints with the CUDA code. If you can come up with a reaction
coordinate that involves a single distance that would work. You could
even use two distances and make a 2D PMF, but that might be overkill
for an ion. If you provide some more details on what your system is
and what exactly you're trying to see we may be able to provide more
specific advice.
-Dan
>
> Input file:
>
> &cntrl
> 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,
> nrespa=1,
> nmropt=1,
> &end
> &end
> &wt type='DUMPFREQ', istep1=2
> &end
> &wt type='END'
> &end
> DISANG=disang.txt
> DUMPAVE=trial.dist
> LISTIN=POUT
> LISTOUT=POUT
> /
>
> disang.txt:
> &rst
> iat=782,-1,
> 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,
> iresid=0,
> &end
> /
>
>
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Oct 17 2014 - 07:00:02 PDT
