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 pair list range. The error can have two sources:. This error arises if the format of the gro file is broken in some way. The most common explanation is that the second line in the gro file specifies an incorrect number of atoms, causing grompp to continue searching for atoms but finding box vectors.
This may not be an error as such. It is simply informing you that during the energy minimization process mdrun 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 orderof 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.
Further minimization may be achieved by using a different energy minimization method or by making use of double precision-enabled GROMACS. This likely indicates that at least two atoms are too close in the input coordinates, and the forces exerted on each other are greater in magnitude than can be expressed to the extent of the precision of GROMACS, and therefore minimization cannot proceed.
It is sometimes possible to minimize systems that have infinite forces with the use of soft-core potentials, which scale down the magnitude of Lennard-Jones interactions with the use of the GROMACS free energy code. This approach is an accepted workflow for equilibration of some coarse-grained systems such as Martini. Sometimes, when running dynamics, mdrun may suddenly stop perhaps after writing several pdb files after a series of warnings about the constraint algorithms e.
When a system is blowing up i. 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.
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:. Please check the reference manual.
It is recommended to observe the system trajectory prior and during the crash. In some cases, if the system has been equilibrated sufficiently, this error can mean that the pressure coupling constant, tau-p , is too small particularly when using the Berendsen weak coupling method. Increasing that value will slow down the response to pressure changes and may stop the resonance from occurring.
You are also more likely to see this error if you use Parrinello-Rahman pressure coupling on a system that is not yet equilibrated - start with the much more forgiving Berendsen method first, then switch to other algorithms. 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.
Refer to the Blowing Up page for advice on how to fix this issue. Always validate the topologies of newly parametrized species! At minimum, check the magnitudes of charges and the atom types assigned to the ligand against existing moieties in the force field.
Examine the contents of jz4. All of them are very low, suggesting that this topology is of very good quality and can be used directly for our simulation. Perform the conversion with:. This ligand introduces new bonded parameters that are not part of the existing force field, and these parameters are written to a file called "jz4.
We will deal with this file shortly, but it is important to note its existence. The ligand topology is now written to "jz4. Convert this. Next, simply copy the coordinate section of jz4.
Since we have added 22 more atoms into the. There should be atoms in the coordinate file now. Including the parameters for the JZ4 ligand in the system topology is very easy. Just insert a line that says include "jz4. The inclusion of position restraints indicates the end of the "Protein" moleculetype section. 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. 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.
Further minimization may be achieved by using a different energy minimization method or by making use of double precision -enabled GROMACS. Sometimes, when running dynamics, mdrun may suddenly stop perhaps after writing several pdb files after a series of warnings about the constraint algorithms e. 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. The message indicates that some piece of your system is tearing apart hence out of the "cell of their charge group". Refer to the Blowing Up page for advice on how to fix this issue.
This means you tried to run a parallel calculation, and when mdrun tried to partition your simulation cell into chunks for each processor, it couldn't.
The minimum cell size is controlled by the size of the largest charge group or bonded interaction and the largest of rvdw , rlist and rcoulomb , some other effects of bond constraints, and a safety margin.
Thus it is not possible to run a small simulation with large numbers of processors. So, if grompp warned you about a large charge group, pay attention and reconsider its size. If you didn't think you were running a parallel calculation, be aware that from 4. Log in Register. All pages Main pages. Documentation of ou Acceleration and par Cut-off schemes. Floating Point Arith Include File Mechani Files with the gro file extension contain a molecular structure in Gromos87 format. This format is fixed, ie.
Columns contain the following information from left to right :. Note that separate molecules or ions e. Note that this is the format for writing, as in the above example fields may be written without spaces, and therefore can not be read with the same format statement in C.
The hdb file extension stands for hydrogen database Such a file is needed by gmx pdb2gmx when building hydrogen atoms that were either originally missing, or that were removed with -ignh. The itp file extension stands for include topology.
These files are included in topology files with the top extension. Use more logfile. The m2p file format contains input options for the gmx xpm2ps program. All of these options are very easy to comprehend when you look at the PosScript tm output from gmx xpm2ps. The format of this file is as follow: first line number of elements in the colormap. Then for each line: The first character is a code for the secondary structure type. Then comes a string for use in the legend of the plot and then the R red G green and B blue values.
In this case the colors are in order of appearance : white, red, black, cyan, yellow, blue, magenta, orange. Below is a sample mdp file. The ordering of the items is not important, but if you enter the same thing twice, the last is used gmx grompp gives you a note when overriding values. Dashes and underscores on the left hand side are ignored.
Note: The parameters chosen e. With this input gmx grompp will produce a commented file with the default name mdout. That file will contain the above options, as well as all other options not explicitly set, showing their default values. Files with the mtx file extension contain a matrix. The file format is identical to the trr format. Currently this file format is only used for hessian matrices, which are produced with gmx mdrun and read by gmx nmeig. The file can be read by most analysis programs, by the graphics program gmx view and by the preprocessor gmx grompp.
Most of these programs create default index groups when no index file is supplied, so you only need to make an index file when you need special groups. First the group name is written between square brackets.
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