[gmx-users] Re: WCA and free energy calculations

Berk Hess gmx3 at hotmail.com
Mon Jun 25 12:09:35 CEST 2007

>From: "David Mobley" <dmobley at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "jtomlins at purdue.edu" <jtomlins at purdue.edu>
>CC: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: [gmx-users] Re: WCA and free energy calculations
>Date: Sun, 24 Jun 2007 16:15:04 -0700
>I'm CCing the users list on this since it might be of general interest.
>>  I
>>can't begin to tell you already how much help you've given me with your 
>>user-list posts and free energy tutorial.
>Glad I can help!
>>I was searching the Gromacs user list and came across a thread by you 
>>tabulated nonbonded interactions and free energy calculations.
>>I'm trying to do exactly the same thing that you described, using the WCA 
>>potential and free energy calculations.  No one ever responded to this 
>>but I was wondering if you figured out the answer?  Also, just to confirm 
>>I'm not spinning my wheels did you get the WCA LJ potential to work using 
>>user specified potential function?
>So, no one ever responded to that thread, as you noticed. But my end
>conclusion was that the tabulated nonbonded interactions know nothing
>about lambda. So while one could implement the WCA separation using
>tabulated nonbonded interactions, one couldn't use it to do free
>energy calculations in a straightforward way, at least not
>simultaneously with the soft core potentials I wanted to use (where
>the effective radius is modified as a function of lambda). So I've put
>it on the back burner for now. I guess you could in principle get WCA
>to work with linear lambda scaing, but there is a lot of work in the
>literature indicating that linear scaling is bad for transformations
>involving insertion or deletion of LJ sites, which is presumably the
>point of using the WCA separation in the first place.
>Anyway -- I think that all means that one would actually need to
>implement WCA into GROMACS to be able to use it for free energy
>I hope this makes sense. Please let me know if any of it needs further
>explanation. Developers are welcome to weigh in if I'm going wrong
>here anywhere...

Tabulated bonded potentials work fine with free-energy!

Or have you tried and they did not work?


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