> I have a question. My system includes a small protein and some > water/ChCl3/Methanol solvents). Before I ran MD, I ran energy > minimization first. However, when I ran MD, the protein jumped out of > the solvent box after 3 ps and the simulation couldn't continue. Who > can tell me what happened? Thank you very much!
Might be an idea to provide more details. Exactly what you did, what the output from the various scripts were when the problem occurred etc. What do you mean by "jumped out of the solvent box"? Note, the box of solvent will typically have PBC, so as a large molecule starts to approach the edge of a box it appears to be outside the solvent, but it isn't, it is sticking into the other side of the solvent box. 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 9073 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. _______________________________________________ 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
