[gmx-users] GROMOS-87 Forcefield Modification
David L. Bostick
dbostick at physics.unc.edu
Thu Oct 25 18:09:09 CEST 2001
The relationship between vdw c6 and c12 is :
c6[i][j] = sqrt(c6[i][i]*c6[j][j])
c12[i][j] = sqrt(c12[i][i]*c12[j][j])
the 1-4 pair interactions are usually taken to be the nonbonded interaction
scaled by 1/8 or 1/6 .. I believe (I think it is 1/8). Many different
modifications are made to the pair 1-4 interactions (other than direct
scaling) to get a reduced effect for 1-4 pairs. I hope this answers the
David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
On Thu, 25 Oct 2001, Christoph Meier wrote:
> Dear all,
> Thanks to everybody who replied to my question about making bonds between protein subunits -
> it is greatly appreciated !
> I have another question:
> In order to improve the implementation of the calcium in my MD simulation, I would to make a few changes
> to the force-field (GROMOS-87), in particular the charges and van-der-Waals
> properties of the atoms in the vicinity of the Calcium.
> I have found descriptions in the literature on how these parameters are affected
> by calcium, but I am having problems including this information in my GROMACS setup.
> In particular, I would like to change the values in the ffgmxnb.itp file.
> Example: Take two atomtypes, O and OA.
> [ atomtypes ]
> ;name mass charge ptype c6 c12
> O 15.99940 0.000 A 0.22617E-02 0.74158E-06
> OA 15.99940 0.000 A 0.22617E-02 0.15062E-05
> [ nonbond_params ]
> ; i j func c6 c12
> O OA 1 0.22617E-02 0.13807E-05
> [ pairtypes ]
> ; i j func cs6 cs12
> O OA 1 0.22617E-02 0.74158E-06
> The Question I have is this: How are the C6 and C12 values of the individual atomtypes
> related to the values found in the 'nonbond_params' and 'pairtypes'.
> In other words: once I have the C6 and C12 values of the atomtypes, how do I get to the
> values in the nonbond_params and pairtypes section ? What's the mathematical relationship between them ?
> It's obvious that some of the values are identical - is this because (in my example),
> the two atoms O and OA are sufficiently similar.
> Or is this a general property of these values ?
> Thank you in advance to anybody who replies,
> Christoph Meier
> Laboratory of Molecular Biophysics
> Department of Biochemistry
> University of Oxford
> South Parks Road
> Oxford OX1 3BW
> Phone +44 1865 275380
> Email christoph.meier at hertford.ox.ac.uk
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