[gmx-users] trjconv and -pbc

[lina]

On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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,
Ha ... stroll?!
> or goes to another side of the protein? Have you looked at the
> trajectory, in particular at the trajectory with the jumps removed?

I extracted the parts from 280ns to 300ns, the presentation of that
part protein is not whole.

In the former way, the time since 280ns till the end,  the small
molecular still outside the cell/box. even the minidist is very small
later.

I am not sure how to get the trajectory and view? (ngmx? )
>

Thanks,
> 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
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