[gmx-users] 3-site methanol model
feenstra at chem.vu.nl
Tue May 20 08:50:01 CEST 2003
Nuno Ricardo Loureiro Ferreira wrote:
> Hi gmx user's
> 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?
AFAIK, the only thing that changes significantly, is the mass. That is
also the only thing I have seen changed by other people. So, simply fill
in the D mass in stead of H mass, and off you go.
Of course, bond strengths ( & vibrations) change, but since these solvent
models are mostly used with constraints (settle/shake/lincs), that falls out
of the simulation. I don't know whether bond *lengths* change significantly
for D versus H.
> 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).
For this type of parameters, within a factor of 10 is good, within 2 is
perfect - I'd say this is perfect agreement (as well as may be expected).
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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