[gmx-users] about solvate
Mark.Abraham at anu.edu.au
Thu May 31 09:37:22 CEST 2007
Rui Li wrote:
> Dear Mark
> Thanks for your reply.
> But I think in the MD process, these original water molecules will move freely,
> even leave the active site. and the new molecules will replace them. Is it
Maybe. Some active sites are closed such that this kind of transition is
impossible over MD timeframes, so you'd definitely want a reasonable
water there to start with, and the crystal water is a good place to
start. Even for more open active sites, you may as well keep the crystal
waters there during system setup to speed the equilibration process...
post-PR equilibration will move them a bit, and if you later see them
exchanging with the rest of the solvent, then that's what you see :-)
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