[gmx-users] PBC - Protein and Ligands

lina lina.lastname at gmail.com
Wed Feb 29 18:19:55 CET 2012

On 1 Mar, 2012, at 1:01, Steven Neumann <s.neumann08 at gmail.com> wrote:

> Dear Gmx Users,
> I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The problem I face is PBC which I cannot get rid of. I used:
> 1.      First make your molecules whole if you want them whole (system).
> trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc
> 2.      Cluster your molecules/particles if you want them clustered
> 3.      Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps.
> trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb
> 4.      Remove jumps if you want to have them removed using the first frame (system)
> trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc
> So the trajecory of my ligands is smooth but they do do bind to the different periodic images. As i know it is impossible to obtain the proper trajectory of all of them I just want to obtain the realistic final positions of my system to extract pdb file for further umbrella sampling. Any suggestions?

You may wanna try 

Trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -ur compact -o pdbs.pdb -dt 1000

Please change dt if necessary. 

> Steven
> -- 
> 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/20120301/84a96d26/attachment.html>

More information about the gromacs.org_gmx-users mailing list