[gmx-users] calculating the pmf in constrained force simulations

Ramya Parthasarathi ramya.sarati at gmail.com
Sat Nov 26 18:17:40 CET 2011


yes exactly thats what I am trying to do.. Thanks a lot for the suggestion
Ramya


On Sat, Nov 26, 2011 at 7:26 AM, <chris.neale at utoronto.ca> wrote:

> Do you mean that you do constrained position simulations and want to know
> how to process the force? If so, read about thermodynamic integration (TI).
> I mostly work with US and position restraints, but for absolute constraints
> I believe that you should take the average force at each constrained
> position and do a trapezoidal integration of the mean force. Surely
> somebody has written a paper on this that you can read.
>
> Chris.
>
> -- original message --
>
> Hi
> I do constrained force simulations and i have the pullf.xvg and pullx.xvg
> files.. I want to know how to calculate the force for each simulation and i
> how to integrate the forces.. can some one help me.
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use thewww interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111126/79997298/attachment.html>


More information about the gromacs.org_gmx-users mailing list