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

[G.H. Zuo]

thanks again.

Guanghong

On Wed, Oct 15, 2008 at 9:10 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> Justin A. Lemkul 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.
>>
>
> The officially blessed version is
>
> trjconv -pbc mol [ -ur compact ]
>
>
>> -Justin
>>
>>
>>> thanks
>>>
>>> Guanghong
>>>
>>>
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>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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