[gmx-users] General questions II

[David van der Spoel]

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}
}


>
>- when you do a simulation in vacuo, Gromacs suggests to use
>  nstcomm=-1, which makes sense. But if you have position
>  restraints, you should not need this ?
No.

>- which of the  com-removal / posres / freeze / pcoupling
>  options are incompatible and why ?
>  (I think what I noticed is that freeze+pcoupl is a very bad idea ..)
Some of the impossible grompp catches but not all.
Freeze + comm removal for instance is not checked for.

I'm sure we haven't tried all combinations

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++