[gmx-users] 3-site methanol model

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Wed May 21 09:32:01 CEST 2003

Hi Nuno,

Nuno Ricardo Loureiro Ferreira wrote:
> Just read van Gunsteren article (JCP, y2000,v112,n23,p10450) about a simple
> three-site model for methanol.  "All" of us agree that the properties of
> P.S. In our lab we use NAMD1.5b1 and GROMACS3.1 ; Tryed a MD simulation with
> 6-site methanol model in a box, with NAMD (500 ps MD, after 1ns
> equilibration), and computed its diffusion coefficient (Dt). The density of
> the box is OK, but the Dt is not so good (298k , Dt exp. = 2.44 10-5 cm2 s-1
> ; Dt obtained = 1.8 10-5 cm2 s-1).

You're lucky. Apparently you have the six-site model already and the
three-site model proposed by van Gunsteren in the paper cited above is
exactly the one which I implemented the gmx-topology for. You can
download it from the molecules section and compare the results.

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

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