[gmx-users] NVE simulations

Anton Feenstra feenstra at chem.vu.nl
Tue Jul 9 09:56:44 CEST 2002

Hi Sidney & David,

If I understood Sydney correctly, he is currently only interested 
in identifying the maximum timestep that he can push in his system. 

This is the same as I and Berk Hess have done in one of my papers:

K. Anton Feenstra, Berk Hess and Herman J. C. Berendsen. Improving
  of Large Time-scale Molecular Dynamics Simulations of Hydrogen-rich
  Systems. (1999) J. Comput. Chem. 20 (8), 786-798 

To determine this maximum time step, you indeed want to monitor energy 
conservation. But that also means you need to eliminate any other 
possible sources of energy drift. The worst of these is cut-offs, but 
there are several others. If I am not mistaken (if so, someone should 
correct me), even when using Ewald, there are residual cut-off like 
effects on the boundary of explicit and long range interactions.

To my knowledge the best method of elminitating all cut-off related
effects is to use a so-called shifted potential, which decays to zero
before the cut-off distance. While this potential introduces other
artefacts, these are not relevant in this case, and it is exactly for
this purpose that there is a shifted potential still implemented in
Gromacs.  This also is the method we used in the paper.

Another energy-drifting source can be the use of constraints (Shake 
sometimes cools the system), but these you cannot readily eliminate 
if you want to push to large time steps. Although I have not actually 
tested this, I would expect Shake-related drift to become worse with 
longer time steps. Generally speaking, the Lincs constraints algorithm 
will be more stable, and definitely is faster, but it is unable to 
handle the highly connected network of constraints in CCl4.

If you really want to push the limit, it would be a good idea to
make a combined dummy mass/dummy atom construction, similar to that
concieved for -NH3 groups in the paper, that would allow Lincs to
be used.

Lastly, as detailed in one of AK Mazur's papers that I cite, 
energy drift is diffusive. To estimate it properly, you need a
fair number of independent runs and average the individual drifts.


 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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