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<P><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">Dear gmx-users</FONT></SPAN>
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<P><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">I'm a novice of GROMACS.</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">I want to simulate for lipid bilayer with antimicrobial peptide.</FONT></SPAN>
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<P><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">I downloaded a lipid pdb from Tielmann's site but I have two questions for MD simulation.</FONT></SPAN>
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<P><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">First.</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">How can I solvate peptide with the lipid pdb ?</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">Editconf and genbox lead some error.</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">I think because the pdb of lipid already formed by box type, but I don't have idea.</FONT></SPAN>
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<P><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">Two.</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">I want to simulate for only lipid using by downloaded pdb.</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">So I proceeded step by step and I succeeded in energy minimization step.</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">When I run restraints MD, I showd an error message as follows.</FONT></SPAN>
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<P><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">"Check for bad contacts and/or reduce the timestep. ~~~"</FONT></SPAN>
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<P><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">Would you tell me what is wrong?</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">I already search gmx_users mailing list but I didn,t hear from list.</FONT></SPAN>
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<P><SPAN LANG="ko"><FONT SIZE=2 FACE="Arial">Thanks.</FONT></SPAN>
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<P><SPAN LANG="ko"><FONT SIZE=2 FACE="굴림">==================================</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="굴림">Jee-Young Lee, Ph.D</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="굴림">Research</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="Arial"> Professor</FONT></SPAN><SPAN LANG="ko"></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="굴림">Bio/Molecular Informatics Center</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="굴림">Konkuk University </FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="굴림">C.P. 82-17-348-2107</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="굴림">e-mail. jyounglee@unitel.co.kr</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="굴림"> </FONT></SPAN><SPAN LANG="en-us"> <FONT SIZE=2 FACE="Arial"> jyoung</FONT></SPAN><SPAN LANG="ko"><FONT SIZE=2 FACE="굴림">@konkuk.ac.kr</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="굴림">==================================</FONT></SPAN>
<BR><SPAN LANG="ko"><FONT SIZE=2 FACE="굴림"> </FONT></SPAN>
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