[gmx-users] 3-site methanol model

Nuno Ricardo Loureiro Ferreira nunolf at ci.uc.pt
Mon May 19 14:55:01 CEST 2003

Hi gmx user's

I want to simulate a peptide in methanol.
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
biomolecules are strongly influenced be the nature of the surrounding
solvent. Some solvent models agree well with some properties and not so well
with others.

My concern is about what model of methanol to use: a six or a three-site
one? My aim is to measure diffusion coefficients of the peptide, and the
methanol that is closer to it. Am I loosing protein information with the
3-site model?

Also, as anibody done MD of deuterated solvents, like D2O, DMSO-d6, CH3OD or
CD3OD? Is there any kind of parametrization done in isotope solvents?

Feel free to answer.
Best regards,

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).

Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra

Phone: +351 239 852080
Fax: +351 239 827703

More information about the gromacs.org_gmx-users mailing list