[gmx-users] Obtaining Positive Energy Values for Both Potential and Total Energies
jalemkul at vt.edu
Wed Jul 23 22:30:19 CEST 2014
I seem to recall others complaining about this topology producing bad energies.
The author of those parameters has never said anything in response, so perhaps
it's a flawed model. With freely downloadable parameters that are not official
Gromacs, caveat emptor!
On 7/23/14, 3:50 PM, Mark Abraham wrote:
> 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 (
>> 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?
>> 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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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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