[gmx-users] Langevin dynamics

[Jia-Lin Lo]

Hi;
     I would like to know how do you perform LD with not explicit solvent.
Did gromacs provide implict solvent model? If not, how did you simulate
the protein with LD method.  How did you make gro and top files.
Thanks in advance.

Jialin



> Tanos wrote:
> >             Hi folks,
> >             I would like to perform a Langevin Dynamics (LD) of 1 ns in
> > a protein of about 900 residues enclosed in a water´s box in physiologic
> > condictions, and I wonder if someone, experienced in this kind of
> > dynamics, has a suitable ld.mdp file to send me.
>
> AFAIK, LD is used when no explicit solvent is included. (The stochastic
> part of LD replaces the solvent bumping into the solute). So, I don't
> see the sense in doing LD on a protein in a water box. Other than
> that, the only differences between MD and LD parameters would be
> the LD friction coefficient which may or may not depend on the (type
> of) protein you simulate.
>
>
> --
> Groetjes,
>
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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