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

[Justin Lemkul]

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!

-Justin

On 7/23/14, 3:50 PM, Mark Abraham wrote:
> Hi,
>
> 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.
>
> Mark
>
>
> 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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-- 
==================================================

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
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================