It should indeed be shifted. Did you write energies each step in md
(ntpr=1)? Otherwise you would not see a match in the mdout file.
On Mon, Jan 4, 2021, 11:51 PM Matthew Guberman-Pfeffer <
matthew.guberman-pfeffer.uconn.edu> wrote:
> 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 Tue Jan 05 2021 - 05:00:02 PST
