Subject: share memory problem for G98 on Linux

From: Yubo Fan <[email-masked]>
Date: Tue, 30 Jul 2002 11:31:00 -0500

Hi, everyone,

A share memory problem has always been bothering me for a long time
since I ran G98 jobs on Linux boxes. Often, I have to kill running jobs
manually to stop optimizations to wrong geometries. I just use "kill -9
'IDs of G98 job'". But, if I killed many times, I couldn't run parallel
jobs any more. Share memory cannot be available at all. I have to
restart the system to clean memory.

Any advice. Thanks in advance

Yubo

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============================================================
Yubo Fan                   Email: [email-masked]
Department of Chemistry    Tel:   1-979-845-7222
Texas A&M University
College Station, TX 77843
============================================================

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From: "J. Zheng" <[email-masked]>
Date: Tue, 30 Jul 2002 10:58:10 -0700 (PDT)

Hi, CCLers:

  My research project is related to protein adsorption on the surfaces.
In order to successfully finish this project, I write a FORTRAN code to
deal with this system which includes protein, explicit waters, counter
ions and surface by using CHARMM force field. Meanwhile, I try to use
CHARMM to handle the same system.

  Now, my program is almost ready for the charged surface. In order to
test the my program, I compared the my results with CHARMM's results for a
protein and water system.  Results are very close. but, my program is 30
times slower than CHARMM!! I use neighbour list to calculate nonbond
interactions, while CHARMM uses cell list to do it. So, my qustions
are

1) Except difference of neighbour list and cell list (I will change to
cell list soon), is there anything I need to pay attention to avoid
expensive calculations when I code program? any trick on the code?

2) Does anybody know how to add a surface to CHARMM? The surface coule be
as simple as charged balls, or as complex as self-assembling
monolayers. I can not find any tutorial or example to show how to do
that from internet.

  Thank for taking your time and energy to read my questions. I will
appreciate for your help.

  Jie

-----------------------------------------------
|  JIE ZHENG                          	      |
|  Department of Chemical Engineering	      |
|  University of Washington		      |
|  Seattle, WA 98105, USA   		      |
-----------------------------------------------
|  Tel:  (206) 616-6510 (o)		      |
| Email: [email-masked]	      |
| Webpg: students.washington.edu/jzheng73     |
-----------------------------------------------

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From: Rick Venable <[email-masked]>
Date: Tue, 30 Jul 2002 19:55:55 -0400

> interactions, while CHARMM uses cell list to do it. So, my qustions

Actually, CHARMM uses a stored neighbor list, which gets updated
frequently (e.g. every 10 or 20 integration steps).  The frequency
depends on the difference between CUTNB (list cutoff) and CTOFNB
(potential forced to zero).  There is a savings from not determining the
non-bond list on every integration step.  

I've been using and writing code for CHARMM for over 15 years, and I'm
not sure what you mean by a "cell list".

CHARMM has a couple different methods for handling boundary conditions,
one of which builds a second list of "image" atoms; these are periodic
replicas of real atoms used for nonbond calculations with real atoms
near the edge of the system.

> expensive calculations when I code program? any trick on the code?

Avoid square roots, division, and trig fxns within inner loops.

> monolayers. I can not find any tutorial or example to show how to do

It depends on what properties you want the surface to have.  For simple
elastic collisions, something like the MMFP module in CHARMM might work.
For more sophisticated interactions with the surface, you might have to
use a planar slab of fixed atoms of the appropriate types.  

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Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   [email-masked]
ALT email:  [email-masked]
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