[gmx-users] waters in ion channels

Nagy, Peter I. PNAGY at UTNet.UToledo.Edu
Fri Jul 3 15:17:46 CEST 2009

You may not want to delete those molecules. It will be interesting to see, whether they stay or leave throughout
the MD simulation after some time. My experience with the Sybyl software was that after some energy minimization (thus removing large forces that could have repelled the waters out the channel) the water molecules 
leave the pore and return to the bulk of the solvent. Then it is a real physical effect, if not an artifact of the applied
force-field or simulation conditions. Nonetheless, I would wait with deleteing these water molecules and see
what happens after, e.g. 200-300 ps.
Best regards
Peter Nagy
Dept. medicnal and Biological Chemistry
The Univ. Toledo,
Toledo, OH, USA


From: gmx-users-bounces at gromacs.org on behalf of Samik Bhattacharya
Sent: Fri 7/3/2009 6:08 AM
To: Gromacs
Subject: [gmx-users] waters in ion channels

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.


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