Hi, I would say that those are water molecule which enter from the bulk water. This is normal and probably important for the physiological function of the system.
Best, Itamar On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharya<[email protected]> wrote: > hi i'm simulating a ion channel protein in DPPC membrane. i'm following > Justin's tutorial for that. and have completed upto the solvation step. but > right after solvation, i found some water molecules in the channel. now i > want to delete those molecules. in the tutorial it is advised tyo use the > keepbyz script to do that.. but after using that i didn't find any change > in the structure. watres are still present in there. may be i am making some > mistake in running the program or something like that!!! can anyone suggest > any thing to solve the problem...thanking you all in advance. > > ________________________________ > Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
