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<DIV dir=ltr><FONT face=Arial color=#000000 size=2>You may not want to delete those molecules. It will be interesting to see, whether they stay or leave throughout</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2>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 </FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2>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</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2>force-field or simulation conditions. Nonetheless, I would wait with deleteing these water molecules and see</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2>what happens after, e.g. 200-300 ps.</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2></FONT> </DIV>
<DIV dir=ltr><FONT face=Arial size=2>Best regards</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2>Peter Nagy</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2>Dept. medicnal and Biological Chemistry</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2>The Univ. Toledo,</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2>Toledo, OH, USA</FONT></DIV></DIV>
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<FONT face=Tahoma size=2><B>From:</B> gmx-users-bounces@gromacs.org on behalf of Samik Bhattacharya<BR><B>Sent:</B> Fri 7/3/2009 6:08 AM<BR><B>To:</B> Gromacs<BR><B>Subject:</B> [gmx-users] waters in ion channels<BR></FONT><BR></DIV>
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<TD vAlign=top>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 <SPAN style="COLOR: rgb(255,0,255)">keepbyz</SPAN> 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.<BR></TD></TR></TBODY></TABLE><BR>
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