Subject: MD simulations in water - Discover

From: Marcin Krol <[email-masked]>
Date: Fri, 7 Jan 2000 11:20:57 +0100 (MET)

Dear All,

I'm trying to perform MD simulations of a protein in a water
solution using Discover (MSI). First of all I simply soaked the molecule
(standard 5A layer of waters) and began the simulation. However, after
~100 ps several water molecules 'evaporated' and the program stopped with
an error message. So I tethered water molecules but it introduces
artificial forces on the protein which limit its conformational
flexibility. I'm also trying a PBC MD simulation but the CPU time of such
calculations is huge. I think that the computationally cheapest  and quite
reasonable would be to run the simulation without explicit water
molecules but to include solvation effects in solvation potentials or
Generalized Born surface area (GB/SA). Is it possible to use GB/SA model
in Discover? Are there any other solutions to the problem of evaporating
waters during the MD simulation?

Thanks in advance for your advice.
Marcin Krol
[email-masked]