On Fri, Dec 7, 2012 at 5:42 AM, dbaogen <dbaogen.gmail.com> wrote:
> Dear all,
>
> Due to the computational speed difference, I would like to use
> pmemd.MPI program rather than snader.MPI to carry out atom position
> restraint MD simulation. Using sander program, the input parameters for
> restraint are set like "ntr=1,restraintmask=':918',restraint_wt=2.0 " .
> Searching the archive in the website, the input parameters for pmemd
> calculation are set like this:
>
If you update to Amber 12, pmemd in that version has the ntr,
restraintmask, and restraint_wt variables available just like sander.
>
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=500000,dt=0.001,
> ntc=2,ntf=2,
> cut=12.0, ntb=2, ntp=1, taup=2.0,
> ntpr=1000, ntwx=1000,
> ntt=3, gamma_ln=2.0,
> ntr=1,
> temp0=310.0,
> /
> 2.0
> RES 918
> END
> END
>
You are missing a title to this group card, and the second atom number in
the RES range (it is _always_ a range). Try the following instead:
&cntrl
imin=0,irest=1,ntx=5,
nstlim=500000,dt=0.001,
ntc=2,ntf=2,
cut=12.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
ntr=1,
temp0=310.0,
/
Restrain residue 918
2.0
RES 918 918
END
END
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Dec 07 2012 - 05:00:02 PST
