[gmx-users] Inserting small molecule into the solvated system
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 "...
> Do you Yahoo!?
> Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
More information about the gromacs.org_gmx-users