Dear Amber Community,
In the spirit of an earlier post <
http://archive.ambermd.org/202010/0428.html>, I’m trying to compute vertical energy gaps. If I run cpptraj with the below lines:
parm complex.prmtop
trajin prod_1.mdcrd
esander RSURF out RSURF.dat cut 10.0 igb 0 ntb 1 ntf 2 ntc 2
run
I obtain energy values that are different from the original output, as compared below.
TOTAL VDW ELEC Bond Angle. Dihedral VDW14 elec14
Origianl MD -569322.9 79197.4 -707668.5 2441.9 6655.1 8500.0 38721.9
ESANDER -569274.9 79236.1 -707657.7 2446.7 6652.0 8497.8 2829.7 38720.5
Difference 48.0 38.6 10.8 4.8 -3.1 -2.2 -1.4
I get the same result as cpptraj if I run sander with imin=5 and ncyc=1. As far as I can tell, the energy value I get from cpptraj are not anywhere in the original MD output, suggesting to me that the values are not simply shifted by some number of frames. Can someone please explain why the energy values are different from the original MD?
Best,
Matthew
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Received on Mon Jan 04 2021 - 21:00:02 PST
