[gmx-users] question about positive potential

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 22 15:05:38 CEST 2009

Baofu Qiao wrote:
> Hi all,
> After a 3ns MD run, I took a look at the  .log file, and found the 
> potential is positive. How could it be?!  I wonder what is the problem.  
> The standard deviation of density is small, while the SD of potential is 
> big. Is the system not equilibrated (if yes, why the sd of density is so 
> small?)?  Or there is something wrong with the force field (I used 
> OPLS-aa, while some parameter of sulfonate are taken from Ionic liquid 
> publication, because I didn't find related parameters)? Or something 
> else I have no idea?  How to solve it?

Your bonded terms are much larger in magnitude than your nonbonded 
potentials. It's hard to diagnose when you haven't told us anything 
about the contents of your simulation system.

> PS: A subsequent md at lower temperature (340K) gives negative 
> potential, however the sd of potential is still quite big: -819(+-)231 
> kJ/mol.

Thus it would seem your force field may be unsuited to elevated 


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