[gmx-users] trjconv and -pbc

[Tsjerk Wassenaar]

Hi Lina,

Make sure to use a reference in which the molecules are together (clustered)
the way you want them.

Cheers,

Tsjerk

On Oct 27, 2011 11:47 AM, "lina" <lina.lastname at gmail.com> wrote:

Hi,

I have a problem using

trjconv_g -pbc nojump
or

trjconv_g -pbc nojump -center

I even tried the -pbc whole.

The system is protein with a small molecular, for the first time
period, when I checked on pymol.
they are together, but later they apart, after show cell, protein
inside the cell, while this small molecular outside,

I did not meet such issue before, it's used  to be easy to fix the pbc
problem, but not this one. a bit surprise,

They are supposed to be together,

Thanks for any advice,
--
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/20111028/6600543c/attachment.html>