[gmx-users] The problem of converting CGenff parameters to those of Gromacs
Peter C. Lai
pcl at uab.edu
Mon Oct 15 16:53:29 CEST 2012
Isn't Mark's script outdated for this purpose?
charmm forcefields specify epsilon and sigmas so you only need to convert
gromacs(sigma) = (charmm(Rmin/2)/10) * (2/(2^(1/6)))
gromacs(epsilon) = charmm(eps) * 4.184
For 1-4 pair interactions,
gromacs(sigma1,4 i,j) = (charmm(Rmin/2_1,4_i) + charmm(Rmin/2_1,4_j))/(2^1/6)
gromacs(eps1,4 i,j) = sqrt(charmm(eps_1,4_i) * charmm(eps_1,4_j)) * 4.184
On 2012-10-15 07:27:51AM -0700, spin wrote:
> Hello, everyone.
> I used the Mark's script's to convert the CGenff (version 2b7 ) parameter
> file to Gromacs .itp files. In the ffcharmmnb.itp, the script gave the c6
> and c12, while the charmm's ffnonbond.itp showed epsilon and sigma.I do not
> understand the relation between the c6/c12 and epsilon and sigma, and I
> have a poor Perl skill. Can someone give me a solution? In addition, the
> script makes all atoms' charge zero in the file, which is not the case in
> the ffnonbond.itp. Why is it?
> Thank you!
> Qing Liu
> View this message in context: http://gromacs.5086.n6.nabble.com/The-problem-of-converting-CGenff-parameters-to-those-of-Gromacs-tp5002042.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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