[gmx-users] Re: Test particle insertion extra coordinate

João M. Damas jmdamas at itqb.unl.pt
Mon Mar 5 00:20:35 CET 2012

Hello MPID (?),

Sorry, I did not see your first message.

For the tpic algorithm, the coordinate of insertion is the last coordinate
(after the particle to be inserted) in the .tpr you give for the mdrun
-rerun. Hence, you should create a structure file (.gro) with the original
system, followed by the particle to be inserted, and lastly, the coordinate
of insertion. Run this structure file through grompp to generate a .tpr
file, which you shall give to mdrun.

I hope this has helped.


On Sun, Mar 4, 2012 at 10:43 PM, MPID <mpmcgovern at wisc.edu> wrote:

> If no one knows this, does anyone know the best way to add a coordinate to
> a
> trajectory in general?
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546083.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> 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

João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120304/5d49d47c/attachment.html>

More information about the gromacs.org_gmx-users mailing list