[gmx-users] LJ System (reduced units) Tar files

PAUL NEWMAN paulclizana at gmail.com
Wed Jul 12 14:52:00 CEST 2006

Dear Gromacs Users:
Sorry I didn't post together the tar file and the tex in the 2 previous
mails. Anyway here you are.
I have a question and I hope you can help me. I want to simulate a LJ-system
in reduced units to reproduce the values of Mol. Phys. 78, 591-618 (page
595). I made my grompp.mdp, conf.gro and topo1.top (Please see attached
file) and I  simulated the system and I got the value close to the right
pression, but the answer was wrong  for the 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? . What i did is:

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

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

   -  topo1.top.- I set up  epsilon=1, sigma=1 and mass=1, following the
   manual reference.

 Could someone help me? Has Anybody done any simulation in reduce
units?, Thanks in advance.

P.S.: gromacs gives the pression in bar ===> presion [in reduced units ]  =
16.6054*pression (in md.log  file)


 g943189 at oz.nthu.edu.tw / paulclizana at gmail.com
National Tsing Hua University (ÇåÈA´óŒW)

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