[gmx-users] Obtaining Positive Energy Values for Both Potential and Total Energies

Mark Abraham mark.j.abraham at gmail.com
Wed Jul 23 21:50:33 CEST 2014


A well-constructed condensed-phase simulation would generally have negative
potential and total energies, but you have too many variables to tell where
the problem is. Start with a single octanol in NVE and a large box and see
how you go.


On Tue, Jul 22, 2014 at 11:12 AM, Yip Yew Mun <yipy0005 at gmail.com> wrote:

> Hi, I have recently downloaded the octanol solvent topology from GROMACS (
> http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies)
> and I was equilibrating it at NPT, and I observed that the Potential and
> Total Energies are positive to 10^4 values. I checked the density and it
> seems fine. There are no warning or abrupt ceasing of the equilibration run
> due to system blow-up. Therefore, I wish to ask if it’s normal to observe
> such trends for those energy values?
> Thanks.
> Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry &
> Biological Chemistry
> School of Physical & Mathematical Sciences | Nanyang Technological
> University | Singapore 639798
> Tel: (+65) 97967803 | Email: yipy0010 at e.ntu.edu.sg | GMT+8h
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