<br><font size=2 face="sans-serif">Hi, </font>
<br>
<br><font size=2 face="sans-serif">I have noticed that the conversion factor
used in gromacs from kcal/mol to kJ/mol is </font>
<br><font size=2 face="sans-serif">4.1868 instead of 4.184 when I was checking
the OPLSAA torsion parameters in gromacs </font>
<br><font size=2 face="sans-serif">database. Then I found it is true for
the bond stretching parameters as well. </font>
<br><font size=2 face="sans-serif">Is there a particular reason for this
4.1868 J/cal conversion factor, or am I missing something </font>
<br><font size=2 face="sans-serif">here? It is a not a huge difference,
but I thought the standard conversion factor should be </font>
<br><font size=2 face="sans-serif">1kcal/mol = 4.184 kJ/mol.</font>
<br>
<br><font size=2 face="sans-serif">Here are two examples. Gromacs converts
the OPLSAA torsion parameters to the five-term </font>
<br><font size=2 face="sans-serif">Ryckaert-Bellemans form. The formular
is</font>
<br>
<br><font size=3><tt> C0=V0+V2+0.5(V1+V3)<br>
C1=0.5(3*V3-V1)<br>
C2=-V2<br>
C3=-2V3<br>
C4=0<br>
C5=0</tt></font>
<br>
<br><font size=2 face="sans-serif">1. Torsion CT-CT-CT-CT:</font>
<br>
<br><font size=2 face="sans-serif">GROMACS:</font>
<br><font size=2 face="sans-serif">CT CT CT
CT 3 2.93076 -1.46538
0.20934 -1.67472 0.00000 0.00000 ; hydrocarbon
</font>
<br><font size=2 face="sans-serif">OPLSAA (2000):</font>
<br><font size=2 face="sans-serif">CT-CT-CT-CT
0.000
1.300 -0.050 0.200 hydrocarbon</font>
<br>
<br><font size=2 face="sans-serif">A quick check C2/(-V2) = 0.20934 kJ/mol/(0.05
kcal/mol) = 4.1868 kJ/kcal <====== </font>
<br>
<br><font size=2 face="sans-serif">2. Bond CT-NT:</font>
<br>
<br><font size=3><tt>GROMACS:</tt></font>
<br><font size=2 face="sans-serif"> CT NT
1 0.14480 319871.5 ; -idem-</font>
<br><font size=2 face="sans-serif">OPLSAA (2000):</font>
<br><font size=2 face="sans-serif">CT-NT 1.448 382.0</font>
<br>
<br><font size=2 face="sans-serif">319871.5 kJ/mol/nm^2 / (2 x 382.kcal/mol/A^2)
= 4.1868 kJ/kcal <=========</font>
<br>
<br><font size=2 face="sans-serif">Thanks.</font>
<br>
<br><font size=2 face="sans-serif">Ruhong</font>
<br>
<br><font size=2 face="sans-serif">Ruhong Zhou, PhD</font>
<br><font size=2 face="sans-serif">Computational Biology Center <br>
IBM Thomas J. Watson Research Center <br>
Yorktown Heights, NY 10598 <br>
Tel: (914) 945-3591, Fax: (914) 945-4104 <br>
http://www.research.ibm.com/people/r/ruhong <br>
</font>