**From:** Fotis Baltoumas (*fbaltoumas_at_biol.uoa.gr*)

**Date:** Fri Jul 17 2015 - 08:47:55 CDT

**Next message:**Simon Kit Sang Chu: "VDW energy diverged & VMD functions applied on cluster"**Previous message:**Branko: "Re: nvt input file"**In reply to:**Charlesworth, Henry: "what exactly is the form of the cosine angle potential?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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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