On Thu, Apr 11, 2002, Monica wrote:
> I am running Simulated Annealing on DNA hexamer.My input
> file is:
> ----------------------------------------------------------------------------
> simulated annealing protocol, 63.5 ps
>
> &cntrl
> imin=0, ntx=1, nstlim=63500,
> temp0=100.0, tempi=100.0, igb=3
> ntt=1, ntb=0, ntf=1, nmropt=1, vlimit=20,
> ntpr=1000, ntt=1, ntwx=2544, ntwv=2544, ntwe=2544,
> cut=10.0, scee=1.2,
> &end
> #
> #Simple simulated annealing algorithm:
...rather non-simple annealing algorithm follows....
> but finally when I view structure it is distorted.
It is not possible to provide a very useful answer from just the complaint
"the structure is disordered...." without knowing what your restraints are,
how distorted it really is, etc. But you might think about the following:
(1) If you heat DNA up to 1000 degrees or more, and don't have *lots* of
stringent constraints, it will almost certainly not anneal back down to
a non-distorted structure. (Of course, this may not apply to you if your
constraints are very detailed.)
(2) Try much simpler runs: just run at 300K with your constraints: what
happens? Just heat to 500K, then cool back down, etc. It is unlikely
that there is a generic answer to your question that anyone on the list
will know...you need to experiemnt to see how your system behaves.
...good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Fri Apr 12 2002 - 09:27:10 PDT
