Re: Non Bonded Paramters

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Tue Oct 21 2008 - 18:05:22 CDT

Hi Abhijit,

First, I recommend you look up combination rules (Lorentz-Berthelot)
somewhere - that's how NAMD behaves by default. Then, the following
namd-l thread should give you information about how to implement your
specific pair interactions:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4855.html

Best,
Jerome

On Tue, Oct 21, 2008 at 6:25 PM, abhijit ramachandran
<abhi_adroit_at_yahoo.com> wrote:
> 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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