gromacs常见错误

The vast 巨大的majority of error messages generated by GROMACS are descriptive解释的, informing the user where the exact error lies. Some errors that arise are noted

below, along with more details on what the issue is and how to solve it.

1. 1. General

1. 1.1. Cannot allocate memory

2. 2. pdb2gmx

1. 2.1. Residue 'XXX' not found in residue topology database

2. 2.2. Long bonds and/or missing atoms

3. 2.3. Chain identifier 'X' was used in two non-sequential blocks

4. 2.4. WARNING: atom X is missing in residue XXX Y in the pdb file

5. 2.5. Atom X in residue YYY not found in rtp entry

3. 3. grompp

1. 3.1. Found a second defaults directive file

2. 3.2. Invalid order for directive defaults

3. 3.3. System has non-zero total charge

4. 3.4. Incorrect number of parameters

5. 3.5. Number of coordinates in coordinate file does not match topology

6. 3.6. Fatal error: No such moleculetype XXX

7. 3.7. T-Coupling group XXX has fewer than 10% of the atoms

8. 3.8. The cut-off length is longer than half the shortest box vector or longer than the

smallest box diagonal element. Increase the box size or decrease rlist

9. 3.9. Unknown left-hand XXXX in parameter file

10. 3.10. Atom index (1) in bonds out of bounds

4. 4. mdrun

1. 4.1. Stepsize too small, or no change in energy. Converged to machine precision, but

not to the requested precision

2. 4.2. LINCS/SETTLE/SHAKE warnings

3. 4.3. 1-4 interaction not within cut-off

4. 4.4. Simulation running but no output

5. 4.5. Can not do Conjugate Gradients with constraints

6. 4.6. Pressure scaling more than 1%

7. 4.7. Range Checking error

8. 4.8. X particles communicated to PME node Y are more than a cell length out of the

domain decomposition cell of their charge group

9. 4.9. There is no domain decomposition for n nodes that is compatible with the given

box and a minimum cell size of x nm

General

Cannot allocate memory The executed script has attempted to assign memory to be used in the calculation, but

is unable to due to insufficient memory.

Possible solutions are:

• install more memory in the computer.

• use a computer with more memory.

• reduce the scope of the number of atoms selected for analysis.

• reduce the length of trajectory file being processed.

• in some cases confusion between Ångström and nm may lead to users wanting

to generate a water box that is 103 times larger than what they think it is (e.g.

genbox).

The user should bear in mind that the cost in time and/or memory for various

activities will scale with the number of atoms/groups/residues N or the simulation

length T as order N, NlogN, or N2 (or maybe worse!) and the same for T, depending on

the type of activity. If it takes a long time, have a think about what you are doing, and

the underlying algorithm (see the manual, man page, or use the -h flag for the utility),

and see if there's something sensible you can do that has better scaling properties.

pdb2gmx

Residue 'XXX' not found in residue topology

残基不存在

database

This means that the force field {you have selected while running pdb2gmx} does not

have an entry in the residue database for XXX. The residue database entry is

necessary both for stand-alone molecules (e.g. formaldehyde甲醛) or a peptide

(standard or non-standard). This entry defines the atom types, connectivity, bonded

and non-bonded interaction types for the residue and is necessary to use pdb2gmx to

build a .top file. A residue database entry may be missing simply because the database

does not contain the residue at all, or because the name is different.

For new users, this error appears because they are running pdb2gmx blindly盲目的

on a PDB file they have without consideration of the contents of the file. A force field is not something that is magical, it can only deal with molecules or residues (building

blocks) that are provided in the residue database or included otherwise.

If you want to use pdb2gmx to automatically generate your topology, you have to

ensure that the appropriate .rtp entry is present within the desired force field and has

the same name as the building block you are trying to use. If you call your molecule

"HIS," then pdb2gmx will not magically build a random molecule; it will try to build

histidine, based on the [ HIS ] entry in the .rtp file, so it will look for the exact atomic

entries for histidine, no more no less.

If you want a topology for an arbitrary molecule, you cannot use pdb2gmx (unless

you build the .rtp entry yourself). You will have to build it by hand, or use another

program (such as x2top or one of the scripts contributed by users) to build the .top

file.