[gmx-users] trjconv and -pbc

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Oct 28 09:15:08 CEST 2011

Hi Lina,

Don't combine fitting, centering and pbc options. It may not work as
expected. That's why the workflow is given. Use separate passes. By the way,
first centering on the protein followed by putting molecules in the box
should also work.



On Oct 28, 2011 9:01 AM, "lina" <lina.lastname at gmail.com> wrote:

On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
wrote: > Hi Lina, >

> Try a _translational_ fit on the protein, follwed by a pass with -pbc
nojump > > Hope it helps,


I tried trjconv_g -fit translation -pbc nojump, ideally it should work.

but still not,

after I tried the minidist, I noticed the peak around 270ns,

I attached the figure, what's the possible reason for this distance?


P.S the box dimension   6.21279   6.21279   6.21279

> > Tsjerk > > On Oct 28, 2011 6:27 AM, "lina" <lina.lastname at gmail.com>
wrote: > > On Fri, Oct 28...

> -- > gmx-users mailing list    gmx-users at gromacs.org >

gmx-users mailing list    gmx-users at gromacs.org
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/b1733cf1/attachment.html>

More information about the gromacs.org_gmx-users mailing list