From: "PAUL NEWMAN" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: [email protected]
Subject: [gmx-users] LJ System (reduced units)
Date: Wed, 12 Jul 2006 20:35:25 +0800
Dear Gromacs Users:
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 rigth
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)
The Boltzmann constant is not 1 in Gromacs, see the manual.
Berk.
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