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

Kay Gottschalk kay.gottschalk at weizmann.ac.il
Thu Jan 8 10:53:00 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.

On Jan 8, 2004, at 11:41 AM, Semen Esilevsky wrote:

>> do you want it on the surface or in the center of
>> the membrane.
>> Either way growing it using free energy methods is
>> probably the safest
>> route. This is not well documented though...
> Could you suggest at list *some* documentation? I'm
> not sure that I understand what does it mean " growing
> it using free energy methods "...
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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science

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