[gmx-users] about solvate

Mark Abraham 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
> correct?

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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