NAMDenergy calculations for nucleic acid systems

From: mon_sharma_at_research.iiit.ac.in
Date: Sat Apr 16 2011 - 03:22:37 CDT

Dear All,
I have done simulations of two similar of RNA systems using Amber parameters. In one case, the pairing of two strands is opening up and in another, it is retained. I wish to calculate the interaction energy between these two strands. I gave one strand as sel1 and another as sel2. This is the configuration file generated using NAMDenergy plugin:
 
amber on
parmfile amb.top
numsteps 1
exclude scaled1-4
1-4scaling 0.833333
scnb 2
outputname namd-temp
temperature 0
COMmotion yes
cutoff 12
dielectric 1.0
extendedSystem namd-temp.xsc
PME on
PMEGridSizeX 86
PMEGridSizeY 101
PMEGridSizeZ 105

switchdist 10
pairInteraction on
pairInteractionGroup1 1
pairInteractionFile namd-temp.pdb
pairInteractionGroup2 2
coordinates namd-temp.pdb
set ts 0
coorfile open dcd namd-temp.dcd
while { ![coorfile read] } {
   firstTimestep $ts
   run 0
   incr ts 1
}
coorfile close

The results I am getting are quite baffling:
1. I am getting positive values for interaction energy.
Frame Time Elec VdW Nonbond Total
0 0 +557.704 -52.757 +504.947 +504.947
1 1 +551.974 -48.4281 +503.546 +503.546
2 2 +541.928 -55.7797 +486.149 +486.149
3 3 +553.588 -53.9855 +499.602 +499.602
4 4 +573.626 -53.0813 +520.545 +520.545
5 5 +570.393 -46.3857 +524.007 +524.007
6 6 +571.145 -47.2915 +523.854 +523.854
7 7 +547.022 -50.7399 +496.282 +496.282
8 8 +539.701 -54.9644 +484.737 +484.737
 

Elec values are all positive. This seems not realistic to me.

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.

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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