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The GROMACS official documentation (see here) states that a system with non-zero total charge will yield an error:

System has non-zero total charge

Notifies you that counter-ions may be required for the system to neutralize the charge or there may be problems with the topology.

If the charge is a non-integer, then this indicates that there is a problem with the topology. If pdb2gmx has been used, then look at the right hand comment column of the atom listing, which lists the cumulative charge. This should be an integer after every residue (and/or charge group where applicable). This will assist in finding the residue where things start departing from integer values. Also check the capping groups that have been used.

If the charge is already close to an integer, then the difference is caused by rounding errors and not a major problem.

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. Nevertheless, it is standard practice to actually add counter-ions to make the system net neutral.

If I understand this correctly, it means that a uniform background charge will be added to a net-charged system. What if I wanted to study a charged system, e.g. a peptide with basic groups in the gas phase, where counter ions are absent. Is it still possible to perform a gromacs calculation on such a system and how will the introduction of the compensating background charge affect the molecular dynamics?

I then looked into other packages and noted that net-charged systems seem to be generally problematic in mm calculations. Can anyone point me into a direction like literature on this?

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    $\begingroup$ A system with net charge is not stable - electrostatic repulsion will make it fly apart. That would seem to be fairly problematic, no? $\endgroup$ – Jon Custer Feb 21 '17 at 15:25
  • $\begingroup$ @JonCuster I am not sure if I understand correctly what you mean: there are tons of systems with a net charge that are incredibly stable. For example, ammonium is a stable ion, a "molecule" with a net charge. In mass spectrometry, you always observe all kinds of molecules with a net charge. So, molecules with a net charge don't fly apart. $\endgroup$ – logical x 2 Feb 22 '17 at 9:18
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    $\begingroup$ A single charged molecule will not fly apart, most likely. Trying to simulate two protons with no electrons will cause you a few problems. So, you need to clarify what your 'system' is since the program is not sentient (yet). If I were writing the documentation, I would probably say something similar - if the user doesn't balance charge on some arbitrary input, the program will do so since it cannot understand what the user really wants to get at. $\endgroup$ – Jon Custer Feb 22 '17 at 14:03
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    $\begingroup$ (Note - I'm just a simple materials scientist - I have no idea what a lysine molecule actually looks like!). I'll ask this question - in biology is the lysine(+1) isolated, or is it in solution? If it is in solution, isn't the system (molecule + surroundings) net neutral? I would think there is an OH- hanging around somewhere? What I do know is various mod/sim techniques have real problems modeling charged defects in solids, and an even harder time modeling charge capture/emission from said defects. Convergence can be very hard in those situations. $\endgroup$ – Jon Custer Feb 22 '17 at 14:17
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    $\begingroup$ The target for most (all?) MD software is biochem and/or materials science, so calculating isolated single molecules charged or not is not their main focus. Your best chance for calculations with periodic boundary condition is using PME or an artificial counterion. $\endgroup$ – Greg Feb 7 '18 at 2:44
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This is intrinsic to Ewald summation methods, not software implementations. The uniform charge arises from neglect of a reciprocal sum term. It does not directly affect the dynamics and may be a reasonable model of a spatially homogeneous system. See https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101544.html for further details and https://www.mpibpc.mpg.de/14063977/Hub_2014_JCTC.pdf for a description and explanation of the likely artefacts.

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  • $\begingroup$ I also suspected that it has something to do with the mm calculation, but that really made it clear. Thanks! $\endgroup$ – logical x 2 Feb 24 '17 at 11:43
  • $\begingroup$ You can also correct for the net charge post simulation $\endgroup$ – Charlie Crown Mar 23 at 0:25
  • $\begingroup$ How would you change the sampling after the fact? $\endgroup$ – mabraham Mar 24 at 2:42
  • $\begingroup$ @mabraham sorry, I didn't get notified you commented, and just saw this randomly. Check out sourceforge.net/p/towhee/mailman/message/24030424. A good question would be... what kind of sampling are you setting yourself up for by putting in an explicit counter ion as is often done? how does that not skew sampling? $\endgroup$ – Charlie Crown Apr 11 at 21:27
  • $\begingroup$ I could imagine such a correction working for e.g. chemical potential. The OP's problem suits using a charged system and they should just do that. However, many cases do not suit that treatment - the sampling of a water box with four chlorides will differ whether four explicit counter ions are present, or not, and so many observable properties will not be able to be corrected by a general correction term. $\endgroup$ – mabraham Apr 13 at 7:06

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