[gmx-users] trjconv and -pbc

[Tsjerk Wassenaar]

Hi Lina,

You first remove the jumps from the trajectory. Then you can view that
trajectory with ngmx or with VMD. You can also then extract the frames
around the 'jump' and look at them. But if the molecule goes unstuck
and then crosses the boundary to get stuck to the protein again, it
would give exactly that result: Visually, the molecule seems close,
goes away and apparently gets stuck somewhere floating nowhere. But
the minimal distance to the protein would be really minimal then go
through a maximum and go to the minimal level again.

Cheers,

Tsjerk

On Fri, Oct 28, 2011 at 12:31 PM, lina <lina.lastname at gmail.com> wrote:
> 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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-- 
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