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 <[EMAIL PROTECTED]> 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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