[gmx-users] LJ System (reduced units)

Berk Hess gmx3 at hotmail.com
Wed Jul 12 14:51:13 CEST 2006

>From: "PAUL NEWMAN" <paulclizana at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>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 
>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.


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