Hi Mark,<br><br>I do not quite understand. For example, in amber ff, 1-4 interactions (except the part from dihedral interactions) are calculated according to non-bonded parameters and then scaled by 1/2 or 5/6. When setting nrexcl = 3, which is the default, aren't 1 - 4 interactions excluded from using non-bonded parameters?<br>
<br>Thanks,<br>Yun<br><br><br><div class="gmail_quote">On Wed, Dec 14, 2011 at 4:33 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><div> </div><div> </div><span>On 15/12/11, <b>lq z </b><<a href="mailto:lqz.fsu@gmail.com" target="_blank">lqz.fsu@gmail.com</a>> wrote:</span>
<blockquote style="BORDER-LEFT:#00f 1px solid;PADDING-LEFT:13px;MARGIN-LEFT:0px" 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><div>Whatever value pdb2gmx generates for CHARMM, probably 3. </div><div class="im"><div> </div><blockquote style="BORDER-LEFT:#00f 1px solid;PADDING-LEFT:13px;MARGIN-LEFT:0px" 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><div>... but 1-4 interactions are regarded as bonded interactions. </div><div class="im"><div> </div><blockquote style="BORDER-LEFT:#00f 1px solid;PADDING-LEFT:13px;MARGIN-LEFT:0px" type="cite">so I should use nrexcl = 2. However, it is 3 in charmm27.ff/ folder.</blockquote>
<div> </div></div><div>Yes, CHARMM has special parameters for some 1-4 interactions, which are dealt with seperately.</div><div class="im"><div> </div><blockquote style="BORDER-LEFT:#00f 1px solid;PADDING-LEFT:13px;MARGIN-LEFT:0px" type="cite">
<div><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><div>As expected.</div><div> </div><font color="#888888"><div>Mark </div>
</font><br>--<br>
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