<DIV> </DIV><DIV> </DIV><SPAN>On 15/12/11, <B class=name>Yun Shi </B><yunshi09@gmail.com> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAHktH24q-h+HDFkSYC3t8x92yVRWHCnZnDyoYHGASDTd_VqSQQ@mail.gmail.com type="cite">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.</BLOCKQUOTE>
<DIV> </DIV><DIV>Yes, see discussion of gen-pairs in manual section 5.7.1 </DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAHktH24q-h+HDFkSYC3t8x92yVRWHCnZnDyoYHGASDTd_VqSQQ@mail.gmail.com type="cite"> When setting nrexcl = 3, which is the default, aren't 1 - 4 interactions excluded from using non-bonded parameters?</BLOCKQUOTE>
<DIV> </DIV><DIV>This is a separate mechanism. Exclusions for non-bonded interactions are applied "on the fly" in mdrun. That doesn't apply to 1-4 parameter generation, but it is necessary for the set of choices of nrexcl, gen-pairs, fudgeXX, [atomtypes], [nonbond_params], [pairtypes] and [pairs] to be consistent. Details vary with the particular force field. Parameters for "bonded" 1-4 interactions (a.k.a. pairs) are generated in grompp according to the rules of the force field - either from the [pairtypes], [pairs] or from scaling depending on the force field and interaction type.</DIV><DIV> </DIV><DIV>Mark </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAHktH24q-h+HDFkSYC3t8x92yVRWHCnZnDyoYHGASDTd_VqSQQ@mail.gmail.com type="cite">
<DIV class="mimepart text html"><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 style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class=gmail_quote>
<DIV class=im>
<DIV> </DIV><DIV> </DIV><SPAN>On 15/12/11, <B>lq z </B><<a href="mailto:lqz.fsu@gmail.com" target=1 >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 />gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" >gmx-users@gromacs.org</A><br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=1 >http://lists.gromacs.org/mailman/listinfo/gmx-users</A><br />Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=1 >http://www.gromacs.org/Support/Mailing_Lists/Search</A> before posting!<br />Please don't post (un)subscribe requests to the list. Use the<br />www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" >gmx-users-request@gromacs.org</A>.<br />Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target=1 >http://www.gromacs.org/Support/Mailing_Lists</A><br /></BLOCKQUOTE></DIV><br /></DIV></BLOCKQUOTE>
<DIV> </DIV>