[AMBER] Inconsistency in energy values between out files and cpptraj

From: SHAUNAK BADANI <shaunak.badani.research.iiit.ac.in>
Date: Sat, 7 Mar 2020 11:56:38 +0000

Hi all,
      I have followed the NEB tutorial given online, using the simulated annealing protocol. I noticed that in the `out` files generated, there were certain energy values printed for all replicates. When I tried to get the energy values using the prmtop file, restart files and cpptraj package in AmberTools, those values differed from out file energies. For one particular image, value given by out file = -228095.0416, while value given by cpptraj = -154996.9489. Does the out file also include potential energies of the spring forces in it? Also, even if it did, shouldn't potential energy of the spring be positive, so as to give an overall energy in the out file > -154996.9489 ?

Shaunak Badani,
3rd year undergrad at IIIT Hyderabad.

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Received on Sat Mar 07 2020 - 04:00:02 PST
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