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If separate coupling groups are required to avoid the "hot solvent cold solute" problem, then ensure that they are of "sufficient size" and combine molecule types that appear together within the simulation. For example, for a protein in water with counter-ions, one would likely want to use Protein and Non-Protein. This error is generated in the cases as noted within the message. The dimensions of the box are such that an atom will interact with itself when using periodic boundary conditions , thus violating the minimum image convention. Such an event is totally unrealistic and will introduce some serious artefacts.
The solution is again what is noted within the message, either increase the size of the simulation box so that it is at an absolute minimum twice the cut-off length in all three dimensions take care here if are using pressure coupling, as the box dimensions will change over time and if they decrease even slightly, you will still be violating the minimum image convention or decrease the cut-off length depending on the force field utilised, this may not be an option.
You should check the spelling of XXXX and look for typographical errors. This error is fairly self-explanatory. You should look at your. That is, you cannot include another molecule type. Consult the examples in chapter 5 of the manual for information on the required ordering of the different [sections].
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Pay attention to the contents of any files you have included with include directives. This error can also arise if you are using a water model that is not enabled for use with your chosen force field by default.
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The reason is that, in spc. You can either add this section yourself, or use a different water model. This error usually indicates that the order of the topology file does not match that of the coordinate file. When running grompp , the program reads through the topology, mapping the supplied parameters to the atoms in the coordinate file. If there is a mismatch, this error is generated. To remedy the problem, make sure that the contents of your [ molecules ] directive matches the exact order of the atoms in the coordinate file.
In some cases, the error is harmless. For example, when running simulations with the MARTINI force field , the workflow relies on grompp to apply the correct names, which are not previously assigned. Also, perhaps you are using a coordinate file that has the old pre In this case, allowing grompp to re-assign names is harmless.
For just about any other situation, when this error comes up, it should not be ignored.
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Just because the -maxwarn option is available does not mean you should use it in the blind hope of your simulation working. It will undoubtedly blow up. This error warns that some combination of settings will result in poor energy conservation at the longest cutoff, which occurs when charge groups move in or out of neighborlist range. The error can have two sources:. A similar error "The sum of the two largest charge group radii X is larger than rlist" can arise under two circumstances:. This error arises if the format of the. The most common explanation is that the second line in the. This is not an error as such.
It is simply informing you that during the energy minimization process it reached the limit possible to minimize the structure with your current parameters. It does not mean that the system has not been minimized fully, but in some situations that may be the case. If the system has a significant amount of water present, then an E pot of the order of 5 to 6 in conjunction with an F max between 10 and kJ mol -1 nm -1 is typically a reasonable value for starting most MD simulations from the resulting structure.
The most important result is likely the value of F max , as it describes the slope of the potential energy surface, i. Only for special purposes, such as normal mode analysis type of calculations, it may be necessary to minimize further. Sometimes, when running dynamics, mdrun may suddenly stop perhaps after writing several pdb files after a series of warnings about the constraint algorithms e.
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When a system is blowing up i. This doesn't necessarily mean you need to troubleshoot the constraint algorithm. Usually it is a sign of something more fundamentally wrong physically unrealistic with your system. See also the advice here about diagnosing unstable systems.
Some of your atoms have moved so two atoms separated by three bonds are separated by more than the cut-off distance. This is BAD. Most importantly, do not increase your cut-off! This error actually indicates that the atoms have very large velocities, which usually means that part of your molecule s is are blowing up.
There can be a number of reasons for the large velocities in your system. If it happens at the beginning of the simulation, your system might be not equilibrated well enough e. Try a nother round of energy minimization to fix this. Experiment with these parameters until the error stops occurring. If this doesn't help, check the validity of the parameters in your topology! Not an error as such, but mdrun appears to be chewing up CPU time but nothing is being written to the output files.
There are a number of reasons why this may occur:. This means you can't do energy minimization with the conjugate gradient algorithm if your topology has constraints defined - see here. This can mean that the system isn't equilibrated sufficiently before using pressure coupling. It is recommended to observe the system trajectory prior and during the crash. Increasing that value will slow down the response to pressure changes and may stop the resonance from occuring. This error can also appear when using a timestep that is too large, e. This usually means your simulation is blowing up.
This is another way that mdrun tells you your system is blowing up. If you have particles that are flying across the system, you will get this fatal error.