<DIV> </DIV><DIV> </DIV><SPAN>On 15/12/11, <B class=name>lq z </B><lqz.fsu@gmail.com> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAJLK-9Wfk=KHrLUr9KCmSG=qZ5=gOfVauPKOPTUBK+iKLtYvzA@mail.gmail.com type="cite">Dear GMXers,<br /><br />I need to use charmm ff (same question for amber ffs), and am confused with what value I should give to nrexcl in [ moleculetype ], 2 or 3?</BLOCKQUOTE>
<DIV> </DIV><DIV>Whatever value pdb2gmx generates for CHARMM, probably 3. </DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAJLK-9Wfk=KHrLUr9KCmSG=qZ5=gOfVauPKOPTUBK+iKLtYvzA@mail.gmail.com type="cite"><br /><br />According to the manual (v 4.5), "nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away." In charmm ff, 1-4 interactions are needed and it is "no further than 3 bonds away," </BLOCKQUOTE>
<DIV> </DIV><DIV>... but 1-4 interactions are regarded as bonded interactions. </DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAJLK-9Wfk=KHrLUr9KCmSG=qZ5=gOfVauPKOPTUBK+iKLtYvzA@mail.gmail.com type="cite">so I should use nrexcl = 2. However, it is 3 in charmm27.ff/ folder.</BLOCKQUOTE>
<DIV> </DIV><DIV>Yes, CHARMM has special parameters for some 1-4 interactions, which are dealt with seperately.</DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAJLK-9Wfk=KHrLUr9KCmSG=qZ5=gOfVauPKOPTUBK+iKLtYvzA@mail.gmail.com type="cite">
<DIV class="mimepart text html"><br /><br />By the way, I did a simple test with a dihedral a-b-c-d. Only a and d have charges. If I use nrexcl =3, no electrostatics energy is reported while the value matches with the one calculated by hand when I set nrexcl to be 2.</DIV></BLOCKQUOTE>
<DIV> </DIV><DIV>As expected.</DIV><DIV> </DIV><DIV>Mark </DIV>