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<PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2>1. <?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><o:p><FONT size=2> </FONT></o:p></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2>I’m simulating some different types of membranes using ffgmx for<o:p></o:p></FONT></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2>lipids from gromacs site.<o:p></o:p></FONT></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><o:p><FONT size=2> </FONT></o:p></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2> I plan to use some of the lipid structure and topology files from<o:p></o:p></FONT></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><A href="http://moose.bio.ucalgary.ca/Downloads/"><FONT size=2>http://moose.bio.ucalgary.ca/Downloads/</FONT></A><o:p></o:p></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><o:p><FONT size=2> </FONT></o:p></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2>When I was doing EM and MD of membrane made of POPE lipids I noticed<o:p></o:p></FONT></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2>something strange: distance between atoms H1 and O7 was about 1.3 A for<o:p></o:p></FONT></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2>every lipid.<o:p></o:p></FONT></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><o:p><FONT size=2> </FONT></o:p></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2> I’m not sure if this is correct. Did someone use this pope.pdb and<o:p></o:p></FONT></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2>pope.itp file? <o:p></o:p></FONT></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><o:p><FONT size=2> </FONT></o:p></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2>2. <o:p></o:p></FONT></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><o:p><FONT size=2> </FONT></o:p></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2>I don’t understand why are the parameters for L-J interactions of atom <SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></FONT></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2>types LOS - LNL (in Ffgmx_lipids) different from parameters for OS - NL <o:p></o:p></FONT></SPAN></PRE><PRE><FONT size=2><SPAN lang=EN-US style="mso-ansi-language: EN-US">interactions (in ffgmx).<SPAN style="mso-spacerun: yes"> </SPAN>(the same is in case LOM-LOM and </SPAN><?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:place><SPAN lang=EN-US style="mso-ansi-language: EN-US">OM</SPAN></st1:place><SPAN lang=EN-US style="mso-ansi-language: EN-US"> – </SPAN><st1:place><SPAN lang=EN-US style="mso-ansi-language: EN-US">OM</SPAN></st1:place><SPAN lang=EN-US style="mso-ansi-language: EN-US">)<SPAN style="mso-spacerun: yes"> </SPAN>Should I use parameters from ffgmx for the atoms building head of the lipid in order to keep the right geometry.<SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></SPAN></FONT></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><o:p><FONT size=2> </FONT></o:p></SPAN></PRE><PRE><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=2> Please give me some comment. <o:p></o:p></FONT></SPAN></PRE></BODY></HTML>