<DIV> </DIV><DIV> </DIV><SPAN>On 29/12/11, <B class=name>Olivia Waring </B><owaring@princeton.edu> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CABXeruzC6ArqGN9D-dcMdK7TLj3xE+O7boywd9L9i1ngqQ2Vzg@mail.gmail.com type="cite">I apologize for the truncated message; I pressed send too soon.
<DIV><br /></DIV><DIV>According to the Gromacs manual, pairs cannot be generated automatically for the Buckingham potential,</DIV></BLOCKQUOTE>
<DIV> </DIV><DIV>Where does it say this?</DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CABXeruzC6ArqGN9D-dcMdK7TLj3xE+O7boywd9L9i1ngqQ2Vzg@mail.gmail.com type="cite">but the [ pairtypes ] directive seems to only accept parameters in LJ form (i.e. c6 and c12, instead of a, b, and c6). I've been looking into ways to interconvert between the two potential forms, but haven't found anything... Can anyone who has successfully generated a topology using the Buckingham potential shed light on this issue?</BLOCKQUOTE>
<DIV> </DIV><DIV>You want a 1-4 interaction using Buckingham functional form? If so, I don't think GROMACS supports it. If you're trying to combine bits of force fields that use L-J with bits of force fields that use Buckingham, then that's almost certainly a bad idea.</DIV><DIV> </DIV><DIV>Mark </DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CABXeruzC6ArqGN9D-dcMdK7TLj3xE+O7boywd9L9i1ngqQ2Vzg@mail.gmail.com type="cite">
<DIV class="mimepart text html">
<DIV> </DIV><DIV><br /></DIV><DIV>Thank you so much,</DIV><DIV>Olivia<br /><br />
<DIV class=gmail_quote>On Wed, Dec 28, 2011 at 11:05 AM, Olivia Waring <SPAN dir=ltr><<a href="mailto:owaring@princeton.edu" >owaring@princeton.edu</A>></SPAN> wrote:<br />
<BLOCKQUOTE style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class=gmail_quote>Hello Gromacs users,
<DIV><br /></DIV><DIV>I'm using a Buckingham potential for the nonbonded interactions in my system, so I have the following lines in my forcefield.itp file:</DIV><DIV><br /></DIV><DIV>
<DIV>[ defaults ]</DIV><DIV>; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ</DIV><DIV> 2 1 no 1.0 1.0</DIV></DIV><SPAN class=HOEnZb><FONT color=#888888>
<DIV><br /></DIV><DIV><br /><BR clear=all>
<DIV><br /></DIV>-- <br />
<DIV>Olivia Waring (王维娅)</DIV><DIV>Princeton University '12</DIV><DIV>AB Chemistry</DIV><br /></DIV></FONT></SPAN></BLOCKQUOTE></DIV><br /></DIV><BR clear=all>
<DIV><br /></DIV>-- <br />
<DIV>Olivia Waring (王维娅)</DIV><DIV>Princeton University '12</DIV><DIV>AB Chemistry</DIV><br /></DIV></BLOCKQUOTE>
<DIV> </DIV>