[gmx-users] GROMOS-87 Forcefield Modification

[David L. Bostick]

Hello Christoph,

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
question.

David 

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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
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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,
> Chris
> 
> -----------------------------------------
> Christoph Meier
> Laboratory of Molecular Biophysics
> Department of Biochemistry
> University of Oxford
> South Parks Road
> Oxford OX1 3BW
> U.K.
> Phone  +44 1865 275380
> Email  christoph.meier at hertford.ox.ac.uk
> -----------------------------------------
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