[gmx-users] Problem with positive total energy

Alex nedomacho at gmail.com
Thu Aug 6 08:06:30 CEST 2015

The total energy being positive is absolutely no reason for concern in 
the case of a gas (as opposed to it being positive for e.g. a crystal). 
This has nothing to do with Gromacs, it does exactly what you tell it to.

In an ideal monoatomic gas, the total energy is exactly (3/2)kT, 
additional contributions of second order (van der Waals) and first order 
electrostatics (say, in plasma). As I said before, you know everything 
about the system to do an estimate and compare the sign with your 
simulation and, far more importantly, the actual averages, with 
literature. Unlike bonded systems, in your case one can actually be 
reasonably quantitative about energies.
Noone on this forum will tell you whether your calculation is reliable, 
based on the sign of your total energy for gas. It can and should be 
positive in many cases, especially at 300K.


On 8/5/2015 11:51 PM, Sunil Ghimire wrote:
> I want  to know that positive total energy  for noble gases at 300k in
> equilibrium state is reliable or not?
> On 6 Aug 2015 11:02, "Sunil Ghimire" <ghimiresunil48 at gmail.com> wrote:
>> I simulated the mixture of argon and krypton(400 atoms).After
>> equilibration run with NPT ensemble at temperature 300k and pressure 1 bar
>> with compressibility 1 bar-1, I obtained required density and pressure but
>> the potential energy was negative and total energy was positive.Is it
>> (positive total energy ) matters or not?
>>    Best regards,
>> Ghimire sunil

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