On 5/31/13 1:18 PM, tarak karmakar wrote:
Dear All,
I have a little confusion with the non-bonding parameters conversion from
OPLS-AA to CHARMM in gromacs.
If I see the ffnonbonded.itp in both the cases I get the following numbers
OPLS-GROMACS
Sigma = 0.1644471 nm
Epsilon = (0.875044*4.184) = 3.66118 kJ/mol
.................................................................................................................................................................
CHARMM-GROMACS
Sigma = 0.21114299 nm
Epsilon = 0.06276 kJ/mol
Now, from the charmm27 parameters file I get
CHARMM27
Rmin/2 = 1.18500 Ang
Epsilon = -0.0150 kcal/mol
Converting these charmm parameters to gromacs formate I have to do
following conversions
Sigma = 2^(5/6) * (Rmin/2) = 2^(5/6) * 1.185 = 2.1114299 Ang = 0.2114299 nm
Epsilon = 0.0150 * 4.184 = 0.06276 kJ/mol
....................................................................................................................................................................
So, CHARMM (par_water_ions.prm) to charmm(ffnonbonded.itp) is fine. But the
problem I'm facing to convert the OPLS(ffnonbonded.itp) to
CHARMM(ffnonbonded.itp).
Why should they be the same? They're different force fields, so they have
different parameters.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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