[gmx-users] RE: Free energy protocol
feenstra at few.vu.nl
Wed Jun 15 17:06:42 CEST 2005
bmbbl at leeds.ac.uk wrote:
> Thanks Groetjes.
> I also have a couple of detail questions.
> 1) I should swtich off -DPOSRE option during step 1 and 3, right?
(But it may depend, e.g., if you need posre to keep your system stable.)
> 2) how long, do you think, is suitable to the rerun mdrun in step 3? Can I use
> the same period of time as step 1, e.g. 1.25-2.5 ns?
I'd use the full length of your run in step 1, unless you still have
non-equilibrated behaviour in the beginning that you are not interested in.
> Thanks a lot.
P.S., if you call me 'Groetjes', shall I call you 'Best'? ;-)
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