[gmx-users] waters in ion channels

Samik Bhattacharya samikbhat at yahoo.co.in
Fri Jul 3 12:08:42 CEST 2009

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.

      Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090703/266f5139/attachment.html>

More information about the gromacs.org_gmx-users mailing list