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<DIV><FONT face=Arial size=2>Lars and David,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanks so much for the input! </FONT></DIV>
<DIV><FONT face=Arial size=2>And Lars, that means I'll have
to subtract the 1-4 interaction energy from the QM total before ls-fitting
to the RH dihedral potential form? I'll try doing that.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanks,</FONT></DIV>
<DIV><FONT face=Arial size=2>Jee.</FONT></DIV>
<DIV> </DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=Lars.Schaefer@mpi-bpc.mpg.de
href="mailto:Lars.Schaefer@mpi-bpc.mpg.de">Lars Schaefer</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Wednesday, May 26, 2004 12:35
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] OPLS
question</DIV>
<DIV><BR></DIV>Hi Jee,<BR><BR>as DvdS stated in this list some days ago, you
DO have to include the 1-4 [ pairs ] for the opls FF additionally, although
you use RBDIHS. The manual has to be updated in this respect. <BR>To my
opinion, this also means that you have to think about your
ls-fitting-procedure, because also the 1-4 interactions contribute to the
overall roatational barrier about the specific bonds you investigate, not only
the RB potential (you have to hit the QM electronic energy with the
total FF energy, which - also for the rotation about the bonds -
constitutes more than just the RB potential). However, it might well be a good
1st approach, I guess. (?)<BR><BR>Cheers, Lars<BR><BR><BR>Jee E Rim wrote:<BR>
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<DIV><FONT face=Arial size=2>Hi,</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>I'm trying to put together a topology for a
nicotine analogue molecule using the OPLS forcefield.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>Most of the atom types that I need and the
force field parameters are already in the OPLS force field, except for a
couple of dihedrals. So, I ran a series of single point calculations using
Gaussian98 to get the energies of the configuration with the dihedral angles
changing from 0 to 360, and am attempting to get the dihedral coefficients
by a least-squares fitting to the Ryckaert-Bellemans potential
function. Is this a good way to get the dihedral parameters? I'm using the
optimized geometry I get from Gaussian, and am just changing the dihedral
angles.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>The second question is, in the manual it's
stated that, with the RB potential, the 1-4 interactions must be excluded,
is this also the case when you're using the OPLS force field? And should I
also exclude the 1-4 interactions when I'm using the parameters derived as
above? </FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>Thanks for your help in advance!</FONT></DIV>
<DIV><FONT face=Arial size=2>Jee.</FONT></DIV><PRE wrap=""><HR width="90%" SIZE=4>
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*******************************************************
Lars Schaefer
MPI fuer biophysikalische Chemie
Theoretische und computergestuetzte Biophysik
Abteilung 070
Am Fassberg 11, D-37077 Goettingen
Tel: 0049 551 201-2305, Fax: 0049 551 201-2302
E-Mail: <A class=moz-txt-link-abbreviated href="mailto:Lars.Schaefer@mpi-bpc.mpg.de">Lars.Schaefer@mpi-bpc.mpg.de</A>
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