[gmx-users] potential energy

[Justin Lemkul]

On 1/10/15 4:39 PM, mah maz wrote:
> some solvent in nanotube actually! What do you mean by various energy
> components? In the results, I just have terms for potential, kinetic, total
> energy and conserved energy which are all positive in all steps.
>

That's not possible.  There are a large number of energy terms stored in an .edr 
file.  If you need further help, you're going to have to provide:

1. A full description of the system (what is it, how did you build it, etc)
2. Your full .mdp file
3. The full g_energy output (available options), copied and pasted from your 
terminal

-Justin

> On Sun, Jan 11, 2015 at 12:52 AM, mah maz <mahmaz71 at gmail.com> wrote:
>
>> I see! You are right. But my system is a nanotube not in gas phase. Is it
>> possible in this case?
>> Thanks alot!
>>
>> On Sun, Jan 11, 2015 at 12:40 AM, mah maz <mahmaz71 at gmail.com> wrote:
>>
>>> Thank you Justin!
>>> you mean we can have a stable system with positive potential and total
>>> energy?
>>> Regards,
>>> Mah
>>>
>>> On Sun, Jan 11, 2015 at 12:22 AM, mah maz <mahmaz71 at gmail.com> wrote:
>>>
>>>> Dear all,
>>>> I wanted to know if the potential energy gained by "g_energy -f ener.edr
>>>> -o" the total potential energy of the system or partial ones like vdw
>>>> energy. If it is the total energy, to my knowledge it should be negative,
>>>> and its summation with the kinetic energy should be negative showing the
>>>> stability of the system. In my simulation, potential energy is positive and
>>>> the total energy is a big positive number, but no explosion happened. What
>>>> is the problem?
>>>> thank you!
>>>>
>>>
>>>
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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