Hi,
For historical reasons, the energies printed to MDOUT are 1 time step
ahead of the coordinates (see e.g.
http://archive.ambermd.org/201905/0075.html). If you do energy
post-processing with sander (i.e. imin=5) on that trajectory then the
energies should match exactly (assuming you're using the same cutoffs,
ewald parameters, etc).
-Dan
On Sat, Mar 7, 2020 at 6:56 AM SHAUNAK BADANI <
shaunak.badani.research.iiit.ac.in> wrote:
> 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 ?
>
> Thanks,
> Shaunak Badani,
> 3rd year undergrad at IIIT Hyderabad.
>
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Received on Tue Mar 10 2020 - 09:30:02 PDT
