AMBER Archive (2003)

Subject: Re: AMBER: MD simulations on small molecules immersed in sparse water shell

From: Alfonso Garcia Sosa (atg21_at_hermes.cam.ac.uk)
Date: Tue Sep 16 2003 - 12:08:24 CDT

I use restraints on these water molecules with a small force constant of
less than 1 kcal/mol, which is the usual value placed on protein backbone
atoms to avoid large structure deviations. 

--
Alfonso T Garcia-Sosa, PhD student
Dept. of Pharmacology,
University of Cambridge & Wolfson College, Cambridge UK

On Tue, 16 Sep 2003, Junmei Wang wrote:

>
>
>
>
>
> Dear AMBER users:
>
> I am running non-periodic boundary MD simulations for a set of middle-sized
> molecules (50-100 atoms). Each is immersed in a sparse water shell (10  to
> 20 TIP3P water, generated using solvateshell in LEAP). What is the best way
> to keep solvent molecules from drifting away from the solute along the MD
> simulations? This is no water cap information in the topology files if
> solvent molecules are added using solvateshell instead of solvatecap.
>
> Thanks
>
> Junmei
>
>
>
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