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

ms devicerandom at gmail.com
Sun Jan 30 17:08:01 CET 2011

On 30/01/11 15:41, David van der Spoel wrote:

>>>>> My question is what effect does running a simulation with a charged
>>>>> system have? I recall reading that something related to PME
>>>>> calculations assumes the system is neutral, but it did not specify
>>>>> whether it was referring to MD or EM. From the mailing list, I have
>>>>> only been able to determine that running a charged system in solution
>>>>> makes no sense biologically.
>>>> Some threads elsewhere cover these issues:
>>>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html
>>>> http://archive.ambermd.org/200712/0223.html
>>>> Mark
>> 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).

Can spreading neutralizing charges along the other chain atoms be a 
viable alternative for enough atoms and enough low charge? (e.g. if I 
have 100 atoms and a +5 net charge, adding a -0.05 charge on all others?)

>> From the reading above, it seems that namd/amber implementations
>> already *implicitly* use this kind of compensation by ignoring terms in
>> the summation. Is it the same for GROMACS?
>> thanks,
>> M.
> Gromacs does not ignore any terms in the simulations if I am not
> mistaken. It also computes PME at every step in contrast to NAMD (don't
> know about Amber).


Massimo Sandal, Ph.D.

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