[gmx-users] how can I obtain the potential energy of each atom？
jalemkul at vt.edu
Mon Apr 29 14:24:52 CEST 2019
On 4/29/19 4:29 AM, Zhang Ke wrote:
> Hello Sotirios,
> Thanke you for your suggestion! I had attempted to use gmx_energy with
> the index of each atom as an input. However, gmx_energy just contains
> the interaction energy between the groups and doesn't contain the
> output of the potential energy of the group.
gmx energy has no ability to produce such output, nor does any other
GROMACS tool. How would one define the energy of an atom when all
properties depend on pairwise bonded and nonbonded interactions? I think
any result would have no physical meaning, particularly because no force
field considers such a quantity (which sounds inherently quantum) in its
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users