From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Fri Jul 17 2015 - 08:47:55 CDT
Hello,
It is K(cos(theta)-cos(theta0))^2.
Therefore, if you want to convert parameters from GROMACS itp to
NAMD/CHARMM-like format, you need to divide the original K value by 2.
The same applies to ALL bonded potentials (bonds, angles and impropers),
not just the cosine angle potential.
You can confirm that simply by comparing the K values in the GROMACS and
NAMD versions of the MARTINI FF.
For example, the GROMACS angle between Qa, Na and C1 particles in the DOPS
lipid is the following
[angles]
; i j k funct angle force.c.
2 3 5 2 180.000 25.0
(since GROMACS uses the k/2 version)
while for the NAMD/CHARMM-like format it becomes
Qa Na C1 2.9875717 180 cos
(25 kj/mol = 5.975143403 kcal/mol => 2.9875717 kcal/mol)
> Hi,
>
>
> I was just wondering what the exact form of the cosine angle potential
> described here is:
> http://www.ks.uiuc.edu/Research/namd/2.10/ug/node26.html
>
> MARTINI Residue-Based Coarse-Grain Forcefield (NAMD 2.10 User's Guide)
> MARTINI Residue-Based Coarse-Grain Forcefield (NAMD 2.10 User's Guide)
> Read more...<http://www.ks.uiuc.edu/Research/namd/2.10/ug/node26.html>
>
> Is it K(cos(theta)-cos(theta0))^2 or (K/2)(cos(theta)-cos(theta0))^2?
>
> Thanks,
> Henry
>
-- ******************************************* Fotis A. Baltoumas Phd Candidate, Bioinformatics Postgraduate Programme Department of Cell Biology and Biophysics Faculty of Biology, University of Athens Panepistimiopolis, Athens 157 01, GREECE -------------------------------------- email : fbaltoumas_at_biol.uoa.gr http://biophysics.biol.uoa.gr http://bioinformatics.biol.uoa.gr *******************************************
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