Hi,
This sounds like an imaging artifact. Try using the 'autoimage'
command from a fully-updated AmberTools 12 cpptraj to re-image your
trajectory prior to calculating RMSD.
-Dan
On Fri, Apr 5, 2013 at 12:38 AM, journal.update
<journal.update.gmail.com> wrote:
> Dear Amber users,
>
> I have run pmemd of amber 11 on a large protien-DNA system, and found that the complex move out of water box after ~20 ns, leading to very strange RMSD in the trajactory. Could you help me to this problem? How can I keep the center of mass of protein-DNA in the center of box?
>
> parameters I used in the running
> -------------------------------------
> Production MD
> &cntrl
> imin=0, irest=1, ntx=5, IG=39727,
> nstlim=100000000,dt=0.002, ntc=2,ntf=2,
> ntpr=5000, ntwx=5000,
> cut=8, ntb=2, igb=0,ntp=1, iwrap=1,
> ntt=1, tempi=298.0, temp0=298.0,tautp=2.0,
> /
> ------------------------------------------
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Apr 05 2013 - 09:30:03 PDT
