[gmx-users] Inserting small molecule into the solvated system

Semen Esilevsky yesint4 at yahoo.com
Fri Jan 9 10:24:01 CET 2004

> It probably means that you first have your system
> with membrane and 
> water. In this System, you insert your (small!)
> molecule first in a 
> very unrealistic way: the atoms are bonded to each
> other, but have no 
> non-bonded interactions with the system; that means,
> no charge, no vdW 
> radius. Then you gradually increase the non-bonded
> terms until you have 
> your 'real' molecule. After each increment of the
> non-bonded terms, you 
> equilibrate your system.
> I hope this is a) correct and b) of some help.

Thanks, it sounds reasonable, but how to implement it?

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