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