[gmx-users] Protein is moving out of box.

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Jun 28 16:03:08 CEST 2008


Well, I think it should also be incorporated into (Gromacs) MD
tutorial material. It's on my to do list. I don't think there's much
use in adding a message in the mdrun output (might as well always add
it, not even checking for jumps). It's basic PBC, which, with a bit of
thinking, can be understood/deduced from what's in the manual and on
the wiki. If people don't read that (anybody who does read that will
be excluded from the set of people hereafter referred to by "they"), I
assume they don't read the log file either. They'll simply run the
simulation and if they have a trajectory, will do analysis (visual
inspection) and run into this "problem". If they don't have a
trajectory, we'll probably get a question about step files, ci-values
or something along those lines.

That may be a bit pessimistic, but on the other hand, let's not forget
that there are many students/researchers getting involved in Gromacs
every week and many of them do know how to search archives/wiki and
read a manual. Also, there's a lot of (new) people asking sensible
questions on this list, making it worthwhile to keep answering posts.
And, to be honest, it does sometimes feel good to shout 'RTFM!'
(RTFML, RTFW) when somebody's not doing his homework :p


On Fri, Jun 27, 2008 at 6:32 PM,  <chris.neale at utoronto.ca> wrote:
> While the frequency with which this question is asked does of course say
> something about how diligently some users are searching the list archives
> and using the wiki before posting a question, it remains true that this is
> causing headaches for a significant number of new users. I therefore wonder
> if there is something that can be done to alleviate this. One possibility is
> to automatically detect the occurrence of this during mdrun and have it
> write out a notice to the user along the lines of what is refereed to in the
> wiki at the end of the log file. I am saying, basically, that although this
> is not a bona-fide problem, I still think that it deserves to be 'solved'.
> Chris.
> Browse the archives, check the wiki.
> http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
> Tsjerk
> On Fri, Jun 27, 2008 at 8:06 AM, Bhanu <bhanuiitr at gmail.com> wrote:
> [Hide Quoted Text]
> Hi all,
> am new to Gromacs. I tried a 10 ps simulation with a protein and after the
> run, the protein came out of the box.. is it good or bad? How can I keep the
> protein in the box?
> Waiting for ur reply.
> Bhanu.
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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