[gmx-users] RE: Free energy protocol

[Anton Feenstra]

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?

Normally, yes.
(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.
> Best,
> Binbin


P.S., if you call me 'Groetjes', shall I call you 'Best'?  ;-)

-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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