[gmx-users] energy minimization of a charged system in vacuum

devicerandom devicerandom at gmail.com
Wed Feb 2 18:49:34 CET 2011

On 30/01/11 16:13, David van der Spoel wrote:
> On 2011-01-30 17.08, ms wrote:
>> On 30/01/11 15:41, David van der Spoel wrote:
>>>> Since I have exactly the same needs (charged system in vacuum) I jump
>>>> in...
>>>> In http://www.gromacs.org/Documentation/Errors
>>>> it says:
>>>> Note for PME users: It is possible to use a uniform neutralizing
>>>> background charge in PME to compensate for a system with a net
>>>> background charge. There is probably nothing wrong with this in
>>>> principle, because the uniform charge will not perturb the dynamics.
>>> I'd like to comment that, this is tricky business. If your charges are
>>> spread out homogeneously it may be OK, but in practice this is often not
>>> the case (e.g. side chains on a protein). One should try to avoid this
>>> if at all possible.
>> Oh, this is very bad news. Could you elaborate on that? (I have a CG
>> model where this would be badly needed).

Further info I found with a lazy check on gscholar:


"Although the stability of a trajectory is a necessary condition for 
studying equilibrium observables of a molecular system, it is not a 
sufficient one to guarantee their correctness. The use of lattice 
summation methods implies that periodicity in a system simulated under 
periodic boundary conditions is considered to be an intrinsic property 
of this system. We refer to this choice as Ewald boundary conditions 
(EWBC). There are a number of reasons to expect that the use of EWBC for 
simulating solutions may lead to undesirable side effects. [...] 
Finally, when a non-neutral solute is considered, the use of EWBC 
implicitly introduces a homogeneous background charge that neutralizes 
the unit cell. This charge density will not model realistically the 
charge density arising from a counter-ion atmosphere, because (i) it 
overlaps with solute atoms; (ii) it is independent of the distance to 
the surface of the solute molecule; and (iii) it completely neutralizes 
the solute charge within an arbitrary volume of solution, the volume of 
the unit cell."

I would love to know how the way GROMACS does PME compares with this...


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