[gmx-users] Re: Hamiltonian replica exchange umbrella sampling with gmx 4.6

[Michael Shirts]

Great -- if it doesn't seem to be working the way it should after some
playing around, then submit it as a redmine issue, and I'll take a
look.

On Fri, Mar 8, 2013 at 2:51 AM, Joakim Jämbeck <jambeck at me.com> wrote:
> Dear Michael,
>
> Thank you for your reply.
>
> Yes, it is relatively clear now. Will try to play around with this later today.
>
> Best,
> Joakim
>
>
>> Date: Thu, 7 Mar 2013 08:55:31 -0500
>> From: Michael Shirts <mrshirts at gmail.com>
>> Subject: Re: [gmx-users] Hamiltonian replica exchange umbrella
>>       sampling with   gmx 4.6
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>
>> Hi, Joakim-
>>
>> Hamiltonian exchange only should work if there is a lambda coupling
>> parameter that defines the potential at each state.  You need to
>> define your pulling potential so that the coupling-lambda parameter
>> can be used to define the different pulling location centers along
>> your trajectory.  Does this make it clearer?
> --
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