Re: AMBER: variable not in namelist for Sander input

From: Haizhen Zhong <>
Date: Mon, 21 Jul 2003 14:08:39 -0400 (EDT)

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 "

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

THank you so much for your help!


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: phone: (801) 587-9652 FAX: (801) 585-9119
> \ Offices: BPRP295A / INSCC 418
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Received on Mon Jul 21 2003 - 19:53:01 PDT
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