[gmx-users] A matter on outputting trajectory of gromacs 4.0

[G.H. Zuo]

thank you very much.  I do it by the trjconv.

A new small problem.
I want get a picture that the protein is in the water box.
Now I must get it by two steps.
trjconv ....-pbc whole ...
and then
trjconv ...-pbc atom -ur compact

can I do it in one step?

thinks

Guanghong

On Wed, Oct 15, 2008 at 8:29 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> G.H. Zuo wrote:
>
>> Dear Gromacs Users
>>
>> I download the new gromacs 4.0 and do some tests on protein folding.
>> It seem that there is a matter on outputting trajectory in this version.
>> When the protein is at the boundary of the box, the mdrun will output the
>> protein in some segments.  This matter had never found in the preview
>> versions.  And It seem that the program trjconv can't correct this matter.
>> Is there someone having ideas about this?
>>
>
> I reported this as well, and it has to do with the new domain decomposition
> scheme (thanks, Tsjerk).
>
> http://www.gromacs.org/pipermail/gmx-users/2008-October/036920.html
>
> And yes, trjconv *does* fix the broken molecules; use trjconv -pbc whole
> with your .tpr file.
>
> -Justin
>
>
>> thanks
>>
>> Guanghong
>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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