AMBER Archive (2003)

Subject: RE: AMBER: variable not in namelist for Sander input

From: Yong Duan (yduan_at_udel.edu)
Date: Mon Jul 21 2003 - 13:51:30 CDT

You need to use "iso" in leap when you build the system.
>From what you wrote, nfft3<>nfft2, you probably did not do that. In this
case, sander will assume rectangular box.

yong

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Haizhen Zhong
Sent: Monday, July 21, 2003 2:09 PM
To: amber_at_scripps.edu
Cc: darden_at_gamera.niehs.nih.gov; tec3_at_utah.edu
Subject: Re: AMBER: variable not in namelist for Sander input

Hi there,

After deleting ntwxm, ntwem, the MD runs in Sander at AMBER6. However,
it
seems it started to change the octahedral box to a cubic box, because
teh
density of the input file is 0.7, after several MD runs (ramping
temperature and following equilibration), when I check the coorfinate
file, it looks like to start to change to a cubic box (the density at
the
first snapshots change to 0.35).

The input line for PME is "
 &ewald
 nfft1=90,nfft2=90,nfft3=80,order=5,dsum_tol=0.00005,
 &end
"

Is it because of the default of alpha, beta, gamma set to be 90.0 degree
for a cubic box? If it is YES, what kind of data I should give to alpha,
beta, and gamma to maintain the octahedral box and at the same time
using
PME?

THank you so much for your help!

Haizhen

On Mon, 21 Jul 2003, Thomas E. Cheatham, III wrote:

>
> I tested the input in both AMBER6 and AMBER7...
>
> > ntwxm=0,
> > ntwem=0,
>
> With AMBER6, remove the two variables above. With AMBER7 ndfmin is no
> longer specified in the input. With these changes, the input file
seemed
> to run OK with my system.
>
> Note that my debugging effort was simplified since some compilers /
> namelist implementations are a little more friendly on failure and
specify
> what variable was not recognized. I tested on a SGI...
>
>
> > times and I can not find where the errors are. By the way, can
anyone give
> > me some references on using PME for an octahedral system for
> > metalloprotein (like zinc-containing protein)?
>
> I do not have any references handy, but note that Zinc can be
difficult
> since the pairwise additive force field may not be sufficient to fully
> represent its properties. Despite this, a number of MD publications
have
> used Zn and if you are mostly concerned with the structure, things may
be
> OK. A pubmed search (+molecular +dynamics +zinc) pulled up lot's of
> references...
>
> Good luck,
>
> \ Thomas E. Cheatham, III (Assistant Professor) College of
Pharmacy
> | Departments of Medicinal Chemistry and of University of
Utah
> | Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East,
Room 201
> | & Center for High Performance Computing Salt Lake City, Utah
84112
> |
> | e-mail: tec3_at_utah.edu phone: (801) 587-9652 FAX: (801)
585-9119
> \ http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC
418
>
>
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