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<P><FONT COLOR="#000000" SIZE=2 FACE="Arial">Dear gromacs users,</FONT>
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<P><FONT COLOR="#000000" SIZE=2 FACE="Arial">I want to simulate an alpha-helix in a methane box (I am currently using the G43a2 force field in Gromacs). As far as I can tell, methane is defined in this force field as residue CH4. I have made the methane .top & .gro files and have so far solvated my alpha-helix using the "genbox -cs protein.gro -ci methane.gro" command. </FONT></P>
<P><FONT COLOR="#000000" SIZE=2 FACE="Arial">Unfortunately, the solvation process was not successful as methane molecules were also positioned<I> inside</I> my helix and<I> on top of</I> protein bonds! As a result, subsequent minimization failed. The manual says that gromacs initially checks for solvent-solvent and protein-solvent overlap, but I do not see so for my model.</FONT></P>
<P><FONT COLOR="#000000" SIZE=2 FACE="Arial"> </FONT>
<BR><FONT COLOR="#000000" SIZE=2 FACE="Arial">Any clue about what I could be doing wrong? Are my methane parameters wrong? Do I need a pre-equilibrated methane box prior to solvation? Is there already an available pre-equilibrated methane box in gromacs? </FONT></P>
<P><FONT COLOR="#000000" SIZE=2 FACE="Arial">Thanks!</FONT>
<BR><FONT COLOR="#000000" SIZE=2 FACE="Arial">sara </FONT>
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<P><FONT SIZE=2 FACE="Times New Roman">Dr. Sara Nunez</FONT>
<BR><FONT SIZE=2 FACE="Times New Roman">Dept. of Chemical Design and Synthesis, CAMD group</FONT>
<BR><FONT SIZE=2 FACE="Times New Roman">Solvay Pharmaceuticals</FONT>
<BR><FONT SIZE=2 FACE="Times New Roman">C.J. van Houtenlaan 36</FONT>
<BR><FONT SIZE=2 FACE="Times New Roman">NL-1381 CP Weesp, The Netherlands</FONT>
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