[gmx-users] question about positive potential

Baofu Qiao qiaobf at gmail.com
Fri May 22 15:53:27 CEST 2009

Hi Mark,

There are two polyelectrolytes in my systems: poly(sodium
4-styrenesulfonate) and poly(diallyl dimethyl ammonium chloride). And
Actually sodium and chloride are absent, only the polycation and the
polyanion. I didn't find suitable force field for sulfonate, thus I used
the reported force field in Ionic liquid for sulfonate (which is based
on opls-aa) , and opls-aa force field parameters for the other atoms.

When I add some water into the polyelectrolytes complex systems, 
potential becomes negative.  See the comparison below, (both at 400K)
                  system                              potential, 
kJ/mol            No. of atoms
                  PE+ & PE-                  7.89481e+03(+-347) 
                PE+ & PE-+water:       -3.04580e+04(+-537)           7080
Any other suggestions?

I wonder that is the size of the system related to this problem? and
when the potential is positive, why doesn't the system becomes expanded
(Does positive potential have some physics)?

thanks in advance!

best wishes,
Baofu Qiao

Mark Abraham wrote:
> 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
> temperatures.
> Mark

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