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<DIV><FONT face=Arial size=2>Hello Maria,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>You can do it by two different
methods.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>1) You can increase the default VdW radii of the
lipid atoms in /usr/local/gromacs/share/top/vdwradii.dat file (path
might be different from your system), say 0.5 for carbon, so genbox will not add
the water inside the bilayer. but you will find a gap between lipid head groups
and water molecules which can be resolved after some ps dynamics. (I personally
have not yet got the success ;-) )</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>2) You can write a small script which can delete
these water molecules, I wrote a script for the same if you need contact me
offline.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Hope it will help</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Alok</FONT></DIV>
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style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=mariagoranovic@gmail.com href="mailto:mariagoranovic@gmail.com">maria
goranovic</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Sunday, October 21, 2007 3:57
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] solvate using genbox
results in water in the center ofthe bilayer. How to edit pdb file contents in
gromacs ?</DIV>
<DIV><BR></DIV>
<DIV>Hi</DIV>
<DIV> </DIV>
<DIV>I am using editconf to try to add water layers on either side of my
bilayer. I use the following command:</DIV>
<DIV> </DIV>
<DIV>genbox -cp popc.gro -box 12.47820 12.35940 10.0 -o solvated.gro -cs
spc216.gro -p topology.top</DIV>
<DIV> </DIV>
<DIV>However, because the center of the bilayer region is less dense, a lot of
water molecules are created inside the bilayer.</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>- How does one usually edit pdb files in gromacs, in terms of, for
example, removing water molecules from the center of a bilayer ?</DIV>
<DIV> </DIV>
<DIV>Thank you</DIV>
<DIV> </DIV>
<DIV>-Maria</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><BR>-- <BR>Maria G.<BR>Technical University of Denmark<BR>Copenhagen
</DIV>
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