[gmx-users] General questions II

[K.A.Feenstra]

David van der Spoel wrote:
> 
> On Sat, 15 Dec 2001, Marc Baaden wrote:
> 
> >- what are the largest timesteps people have used with Gromacs ?
> >  and in what conditions ?
> >  (eg maybe 5 fs when using constraint=bond-angles ???)
> 
> 7 fs using dummy particles: see Feenstra et al. JCC 
> @Article{Feenstra99a,
>   author =       {K. Anton Feenstra and Berk Hess and Herman J. C. Berendsen},
>   title =        {Improving Efficiency of Large Time-scale Molecular
>                   Dynamics Simulations of Hydrogen-rich Systems},
>   journal =      BTjcc,
>   year =         1999,
>   volume =       20,
>   pages =        {786-798}
> }

Thanks David ;-)

This goes in conjunction with options I added to pdb2gmx: 
      -dummy   enum   none  Convert atoms to dummy atoms: none, hydrogens or
                            aromatics
 -[no]heavyh   bool     no  Make hydrogen atoms heavy

Simply using constraints on bond angles will not help you, this is
described in the paper. In short, a protein with constraint angles
does not behave like a 'real' protein.

The 'aromatics' constructions were not yet mentioned in the JCC paper
cited above, but will be in an upcoming paper submitted to Proteins.
The idea is simple: at large timesteps the planar groups are inherently
unstable using the normal improper dihedral parameters and tuning them
to 'fit' the time step will cause the groups to become more flexible.
So in stead, we keep only three of the atoms in each group as a 'real'
atom (with mass), and construct the rest of the groups as dummy atoms.
This results in a perfectly stable and planar group at almost any time
step.

Some extensive testing (some of which will be described in yet another
upcoming paper) has indicated that time steps of 4 or 5 fs are unlikely
to yield artefacts. The verdict on 7 fs is still out, there are some
indications that things slightly change, but it is not clear wether this
is significant.

-- 
Groetjes,

Anton
 _____________ _____________________________________________________
|             | Anton Feenstra       Dept. of Biophysical Chemistry |
|  _   _  ___,| K.A.Feenstra at chem.rug.nl    University of Groningen |
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