[gmx-users] trjconv and -pbc

[Tsjerk Wassenaar]

Hi Lina,

My previous reply was from before I looked at the graph. Have you
considered that the molecule might be taking a stroll and turn back,
or goes to another side of the protein? Have you looked at the
trajectory, in particular at the trajectory with the jumps removed?

Cheers,

Tsjerk

On Fri, Oct 28, 2011 at 9:15 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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.
>
> Cheers,
>
> Tsjerk
>
> 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,
>
> Hi,
>
> Thanks.
>
> 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?
>
> Thanks,
>
> 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...
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands