[gmx-users] [Fwd: Gromacs]

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 13 09:06:49 CEST 2006

-------- Original Message --------
Subject: 	Gromacs
Date: 	Wed, 12 Jul 2006 20:14:52 +0800
From: 	PAUL NEWMAN <paulclizana at gmail.com>
To: 	spoel at xray.bmc.uu.se

Dear David van der Spoel:
I have a question about your web site
(http://www.csc.fi/chem/courses/gmx2004/exercises/index.html). You give
files to make a simulation of LJ-system in reduced units (Argon). I
modified them  in orde to reproduce the values of Mol. Phys. 78, 591-618
(reduced temperature= 5, reduced density = 0.4, it's in the attached
file page 595). I simulated the system and I got the value close to the
right pression, but the answer was wrong  for the LJ potential (I got
almost  the potential but times 1000). I tried various other  values and
I got the same thing. I don't know where the error is?. I send you my
grompp.mdp, conf.gro and topo1.top (Please see attached file). What i
did is:

    * grompp.mdp.- I set up reduced temperature= 5, rcut-off =4 (rvdw),
      and Temperature coupling = Berendsen.

    * conf.gro.- I generated the initial positions as SC also in reduce
      units (simple cubic). reduced density = 0.4 (864 atoms and box
      size 12.92660x12.92660x12.92660) .

    *  topo1.top.- I set up  epsilon=1, sigma=1 and mass=1, it 's almost
      the same file in your web site. I just changed the number of
      particles (864 atoms)

But  I can't figure out what is wrong. Could you help me? Have you done
any simulation in reduce units  and checked them out?,if so, If it isn't
too much to ask, could you send them to me . I'm sorry for bothering you
about things, you might think, they are trivial questions. Thanks in

P.S.: gromacs gives the pression in bar ===> presion [in reduced units
]  = 16.6054*pression (in md.log  file). Is it right? I calculated the
pression in this way. And i send you my md.log file.


Paul C.L.
g943189 at oz.nthu.edu.tw <mailto:g943189 at oz.nthu.edu.tw> /
paulclizana at gmail.com <mailto:paulclizana at gmail.com>
National Tsing Hua University (ÇåÈA´óŒW) <http://www.nthu.edu.tw/>

I appreciate your help. Thanks!
Os agradezco la ayuda. Gracias!

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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