[gmx-users] Is it possible to turn off protein-water interaction?

David spoel at xray.bmc.uu.se
Wed May 21 09:02:01 CEST 2003

On Wed, 2003-05-21 at 06:47, Erik Lindahl wrote:
> Hi Ruhong,
> No - you've probably found the concept of energy groups, but they
> cannot yet be applied to individual terms.
> However, you might soon be able to do it using groupwise decoupling
> that I'm implementing for Free Energy calculations.

> I guess this is probably not supported without modifying the source,
> but I will ask it anyway. Is there an easy way to turn off
> protein-water interactions (vdw attraction C6 terms and Coulombic
> interactions), but leave protein-protein and water-water interactions
> untouched? In other words, I don't want any interactions b/w water and
> protein atoms except for the replusive LJ to avoid overlaps. I am
> studying the dewetting phenomena in a multi-domain protein where two
> independent domains fold into a complex structure. It would be nice to
> see what happens if there is no interaction b/w protein and water.  
You can turn off the dispersion by adjusting the parameter matrix.
But... your system would explode if you leave out the compensating
(attractive) terms. It would be best to switch the whole interaction off
with energy_grp_excls (check exact syntax) and add another repulsion
term (e.g. a hard wall, which you would have to program, and you don't
want to scan through all possible interactions).

Now, to understand what would happen if you make the interaction purely
repulsive, my 2 c of prediction say that you would get some kind of
phase separation where contact area is minimized.

> </smaller></excerpt>
Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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