On Mon, Jul 28, 2003, Lishan Yao wrote:
> > On Mon, Jul 28, 2003, Lishan Yao wrote:
> >
> > > I use quasih program to do the entropy calculation for
> > > 6-hydroxymethyl-7,8-dihydropterin.
> >
> > > 1, Those low frequencies are kind of too low. what kind of motion can
> > > have these low frequencies for a small organic molecule. When I use MP2
> > > to do the frequency analysis, I get totally different results.
> >
> > Did you use ptraj to remove overall translation and rotation before running
> > quasih?
> Yes, I think I did. This is what I did:
What you did looks OK to me. You should certainly look at the values in the
rms_to_average_frame.dat file: are they all quite small? You may also need
to visualize the md_nvt23_now_fit.crd trajectory to see if there are any
conformational transitions taking place, etc.
(Or maybe someone else on the list will spot a problem with the ptraj
scripts).
> >
> > > 2. The number of frequencies given by this program is less than or equal
> > > to 3N/2 (Is there any reason behind this?).
Change line 227 in quasih.f from
ncv = 2*nev
to
ncv = min( 2*nev, n )
and recompile. That should help; if so, I'll post a bugfix.
...regards...dac
-
==================================================================
David A. Case | e-mail: case.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
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Received on Mon Jul 28 2003 - 19:53:00 PDT
