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<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; TEXT-ALIGN: justify"><SPAN style="FONT-SIZE: 12pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'">Dear Gromacs Users,<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; TEXT-ALIGN: justify"><SPAN style="FONT-SIZE: 12pt; COLOR: #333333; LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'">I’m interested in n-alkanes and </SPAN><SPAN style="FONT-SIZE: 12pt; COLOR: black; LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'">evaluating thermophysical </SPAN><SPAN style="FONT-SIZE: 12pt; COLOR: #333333; LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'">and structural properties of n- alkanes and binary mixtures of n-alkanes. I want to use Gromacs and the force fields in Gromacs for my n-alkanes simulations. And I want to ask some questions to you. First, I’m planning to generate a packmol pdb file that includes 100 molecules for pure and binary mixtures. Can I directly use this pdb file with <SPAN style="mso-spacerun: yes"> </SPAN></SPAN><SPAN style="FONT-SIZE: 12pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New
Roman','serif'; mso-bidi-font-style: italic">pdb2gmx ? Can I use the partial charges generated with Gaussian for n-alkanes molecules ? If so, what is the procedure of this ? How can I load the partial charges into Gromacs ? And Finally, I want to use both all atom and United atom force fields. Could you suggest me some force fields that can be used for n-alkanes md simulations ?</SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; TEXT-ALIGN: justify"><SPAN style="FONT-WEIGHT: normal; FONT-SIZE: 12pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; mso-bidi-font-weight: bold">Thanks in advance<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; TEXT-ALIGN: justify"><SPAN style="FONT-WEIGHT: normal; FONT-SIZE: 12pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; mso-bidi-font-weight: bold">Kind regards</SPAN><B style="mso-bidi-font-weight: normal"><SPAN style="FONT-SIZE: 12pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'"><o:p></o:p></SPAN></B></P></DIV></div><br>
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