[gmx-users] Steered MD

[Miguel Ángel Mompeán García]

You mean TMD (Targeted Molecular Dynamics). As far as I know, this is not
implemented in GROMACS (hope anyone corrects me if I am wrong)



2012/6/4 Mike M <nmr.mike.nmr at gmail.com>

> Dear Gromacs Users,
>
> I am trying to study the conformational path from state A to state B with
> targeted molecular dynamics. These two states are two different structures
> of a peptide that I have calculated after a series of nmr experiments. I
> have perform 100ns simulations separately of the two peptides to assess
> their stabilty over the course of the simulations, but now I wonder how can
> I direct my system A towards the state named as B. In the manual I have
> read what it is said in the manual about this topic and the usage of -rb to
> provide the coordinates of the B state, but I did not find out how to
> properly set the simulation.
>
> Has anyone done this before?
>
> Thanks,
> Mike
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read 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/20120605/2f1ef164/attachment.html>