Re: [AMBER] [ Error with MD ] Energetics of the system

From: David Case <>
Date: Fri, 10 Jan 2020 13:43:39 +0000

On Fri, Jan 10, 2020, 조준범 wrote:

> 1-4 NB = 1933.8019 1-4 EEL = -1196.6003 VDWAALS =242302019.5467

You vdW energy is enormous, indicating the two atoms are nearly on top
of each other in the starting structure. You can use the "check"
commands in either cpptraj or parmed to identify which atoms are

You indicate that you did "EM" (energy minimization??) first. If so,
see if the energies at the end of the minimzation match those at the
beginning of your dynamics. If they don't match, that may provide a
clue about what is going on. (Of course, if they do match, something
went badly wrong at the minimization step....)


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Received on Fri Jan 10 2020 - 06:00:03 PST
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