All that is entirely due to the PBC. The molecule is simply no longer centered in the box, that is all. It is still entirely surrounded by water.
Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Eugenia Polverini > Sent: Tuesday, 30 January 2007 10:49 PM > To: [email protected] > Subject: [gmx-users] protein goes out from the waterbox during MD > > > Dear all, > in the output of my 5 ns MD of a small protein in a box of water and > pbc, I see that during MD the protein goes out from the box. > Why it happened? Is it a problem or I can accept that all was > OK? I have set the comm_mode=angular. > > Thanks for your help! > Best regards > Eugenia > > > > -- > Eugenia Polverini, Ph.D. > Dept. of Physics > University of Parma > Parco Area delle Scienze, 7/A > 43100 Parma > ITALY > > Phone: +39 0521 905254 > Fax: +39 0521 905223 > E-Mail: [EMAIL PROTECTED] > http://www.fis.unipr.it/~polveri > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
