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

David van der Spoel spoel at xray.bmc.uu.se
Sun Jan 30 16:41:32 CET 2011

On 2011-01-30 16.02, ms wrote:
> On 29/01/11 05:08, Matt Chan wrote:
>> Perfect. This is great reading.
>> Thanks for the pointers Mark.
>> Matt
>> On 01/28/2011 06:50 PM, Mark Abraham wrote:
>>> On 29/01/2011 9:57 AM, Matthew Chan wrote:
>>>> Hi,
>>>> I'm a first time GROMACS user. I've got 2 questions, which I'll ask
>>>> in separate emails. The first is about running EM on a charged
>>>> protein in vacuum.
>>>> I'm presently walking through some of the tutorials and trying to
>>>> simplify them for my purposes. One is the energy minimization of the
>>>> 1AKI lysozyme protein. I would like to minimize this protein in
>>>> vacuum instead of solution as the tutorial demonstrates. Since the
>>>> genion program replaces water molecules with ions to balance the
>>>> charge of the system and there's no water, I'm having trouble running
>>>> the simulation with a neutral system.
>>>> 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.

>  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).

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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