AMBER Archive (2003)

Subject: Re: AMBER: Question about quasih analysis

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Mon Jul 28 2003 - 15:24:19 CDT

Thanks for the help. Now, it works. I get 3N-6 frequencies. I check the
trajectory file, one CH2OH group and one NH2 spin. Probably that is the
reson why I get some low frequencies. My question is : In nature, does
it really spin, or just an artificial phenomenon of MD? My friend, a
quantum chemistry guy, doesn't believe it should spin.

Lishan

On Mon, 2003-07-28 at 14:37, David A. Case wrote:
> 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_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
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-- 
Lishan Yao <yaolisha_at_pilot.msu.edu>
MSU

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