Re: NAMD_energy_plot

From: Jason Swails (jason.swails_at_gmail.com)
Date: Tue Jul 22 2014 - 17:22:29 CDT

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On Jul 22, 2014, at 3:08 PM, sananda chatterjee <sanandabhu_at_gmail.com> wrote:

> Dear all,
> I have performed a MD simulation in NAMD using AMBER force field. I next analysed the energy plot using NAMD plot using the NAMD log file but i am getting positive van der Waals energy ranging from +9500 to +10520.Is there anything wrong having positive values for VDW .

No, there is nothing wrong with that. All it means is that numerous electrostatic attractions are strong enough to draw two atoms closer together than their pair sigma value.

HTH,
Jason

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher

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