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

David van der Spoel spoel at xray.bmc.uu.se
Sun Jan 30 17:13:16 CET 2011

On 2011-01-30 17.08, ms wrote:
> 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).
With homogeneous I mean a solution of ions.
> 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?)
Sounds like a recipe for disaster. Try looking for solutions with 
explicit counter ions.

>>> 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).
> Thanks.
> m.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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