[gmx-users] ED-analysis

[Tsjerk Wassenaar]

Hi Kavya,

>> It is absolutely necessary that the molecules be whole, and in the
>> case of multimers, correctly assembled.
>
> But if there is only one polymer (protein) with water in the system
> then also is it necessary to use nojump or mol in trjconv?because
> in one of the mails -
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html
>
> there was a discussion regarding this topic. So I wanted to
> ensure regarding that aspect. Molecule after simulation
> crosses the box boundary in the simulation I have done, So
> if I processed analyzing with the native .xtc file there will be
> a problem? But in this case its a single intact protein molecule
> in water.

That post concerns -pbc nojump. My reply to you was about having
molecules in one piece. They're different things. Gromacs nowadays
doesn't care about molecules being whole in the trajectory file, and
happily writes them in pieces. So you can't be confident you can use
the trajectory as is.

Cheers,

Tsjerk

-- 
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