Re: NAMDenergy calculations for nucleic acid systems

Date: Sat Apr 16 2011 - 08:18:17 CDT

Hello Peter,

Thank you for reply. Thats what I thought earlier, but the visualization did not seem in correlation with the results. I will
try to look at the interaction without the backbone atoms if I wish to just account for the interaction within bases. I hope that would be fine.

----- Original Message -----
From: "Peter Freddolino" <>
To: "mon sharma" <>
Sent: Saturday, April 16, 2011 4:18:31 PM
Subject: Re: namd-l: NAMDenergy calculations for nucleic acid systems

Hi Monika,

On 04/16/2011 04:22 AM, wrote:

> 1. I am getting positive values for interaction energy.
> Elec values are all positive. This seems not realistic to me.

Why not? You've got two polymers which carry massive negative charges in
close proximity to each other. Considering them in the absence of
counterions should give positive values for electrostatic energy.
> 2. The system where the base pairs are opening up has more favorable values (lesser positive values) than the one which is base paired fine.

See my answer to (1) above. What you're seeing is probably dominated by
the interactions of the backbones with each other.


> I think there is something which I am missing. I am not able to figure out. Please suggest.
> Thanks & Regards,
> Monika Sharma

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