[gmx-users] Longer scale simulations

[ran at hemi.tau.ac.il]

Thanks! I'll certainly read the article and try it.

In case it might be interesting to any of the gmx users, I found a reference by
Fan and Mark, who used this method recently - Proteins, 53 (1):111-120 (2003).

Ran.

Quoting Anton Feenstra <feenstra at chem.vu.nl>:

> In addition, you can use dummified hydrogen atoms. This removes the highest
> frequency motions allowing the timestep to be raised from 2fs to 4-5fs
> giving an additional performance gain of a factor of 2 without noticable
> loss of accuracy. I've described this in J. Comput. Chem. 20 (8),
> pp786-798, 1999, and David and Erik have rigorously tested it recently
> (but I don't have that reference at hand though, sorry). It is also
> already built into pdb2gmx (and grompp), simply by adding '-dummy hydrogens'
> when you run pdb2gmx.
> 
> 
> -- 
> Groetjes,
> 
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
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