Non Bonded Paramters

From: abhijit ramachandran (abhi_adroit_at_yahoo.com)
Date: Tue Oct 21 2008 - 17:25:04 CDT

Hi all,

How do we define new non bonded parameters, i have just started with a 6 atom system but i was trying to define my own set of parameters, i did that for Bonded, but i dont know how to do for nonbonded.

Here is my PDB file:

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 C1 ADNA 1301 -0.000 8.896 2.186 1.00 0.00 Aby
ATOM 2 D1 ADNA 1301 2.365 6.568 1.280 1.00 0.00 Aby
ATOM 3 E1 ADNA 1301 0.575 0.516 0.051 1.00 0.00 Aby
ATOM 1 C2 ADNA 1301 -0.628 -8.896 -2.186 1.00 0.00 Aby
ATOM 2 D2 ADNA 1301 2.365 -6.568 -1.280 1.00 0.00 Aby
ATOM 3 E2 ADNA 1301 0.000 -0.516 -0.051 1.00 0.00 Aby
END

I also generated the PSF file by defining my own topology file but when it comes to non bonded parameters i dont know how to define it since we just type one atom type, i mean we dont mention the pairs.

So if an Atomtype 'D' with a specific epsilon and specific Rmin/2 will react the same way with atome type 'C' (C1 and C2) and atome type 'E', so how do we characterize the interaction say i want 'D' to repel 'C' more as compared to 'E', if both are equally close.

Basically how do I obtain specific non bonded interaction between different atoms.

Thank you for your replies!!!

Abhijit Ramachandran.
Bio-Nano Fluidics Lab.
Department of Bioengineering.
The University of Texas at Arlington
Arlington, TX - 76019

      

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