Re: [AMBER] Error of restraint of atom using "pmemd" program in Amber 11

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 7 Dec 2012 07:30:23 -0500

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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 07 2012 - 05:00:02 PST
Custom Search