Tip
All input files can be downloaded: Files
.
charmm
This keyword defines the implementation details of CHARMM force field.
Options
- parameters
Value
One or more file names
Default
None
Give the CHARMM force field parameter file names (paths may be included). There is no default one so at least one file name must be given. There can be more than one files:
1 charmm 2 parameters par_all35_ethers.prm /home/zhang/userdef/par_all35_proteins.prm 3 end
Note that if the same term, say bond
CT-CT
, appears in more than one parameter files, then the latter one will overwrite the previous ones.
- topology
Value
A file name
Default
None
Give the topology file name of the molecule in PSF format (path may be included).
- scaling14
Value
A real number
Default
1.0
Define the scaling factor for electrostatic interactions of 1-4 term. For most cases, it is set to
1.0
.
- rcutoff
Value
A real number
Default
15.0
Define the distance in Angstrom to cutoff non-bonded interactions.
When
use_PBC
is turned on,rcutoff
should be smaller than the half of periodic box size to avoid self interactions.If
rswitch
is larger thanrcutoff
, switching function will not be used and no cutoff is applied on long range forces.
- rswitch
Value
A real number
Default
10.0
Define the distance in Angstrom to activate switching function.
If
rswitch
is larger thanrcutoff
, switching function will not be used and no cutoff is applied on long range forces.
- use_PBC
Turn on periodic boundary condition for the system. If this option is not present, the system will be a non-periodic, gas phase one.
- Lbox
Value
Three real numbers
Default
0. 0. 0.
When
use_PBC
is present, this option gives the lattice lengths along X, Y, and Z direction in Angstrom.1charmm 2 use_PBC 3 Lbox 86 86 86 4end
This creates a simulation box of 86 Angstrom x 86 Angstrom x 86 Angstrom.
- electrostatic
Value
Cutoff
Cutoff scheme for gas phase or periodic systems.PME
Particle mesh Ewald (PME) method. Only available for periodic systems.Default
Cutoff
Assign the scheme to calculate electrostatic interaction.
For gas phase,
Cutoff
is the only possible way.For MM calculations in periodic systems, both are available and it is recommended to use
PME
.For QM/MM calculations in gas phase or periodic systems,
Cutoff
is currently the only possible way.
- PMEk
Value
Three integers
Default
64 64 64
Assign the number of grids for PME long range force calculations. It is recommended that the number should be chosen as an integer close to the lattice length while is a multiply of only 2,3 and/or 5. For example, if
Lbox
is109. 109. 77
, thenPMEk
can be set to108 108 80
.
Theoretical Background
CHARMM Force Field
To do a CHARMM force field calculation, besides system coordinates, one needs to provide the system topology (by topology
) and force field parameter files (by parameters
). The CHARMM force field is decomposed into bonded interactions and nonbonded interactions. The bonded interactions include bond stretching, angle bending, dihedral angle rotation, and improper torsion. The nonbonded interactions include Lennard-Jones interactions and electrostatic interactions. They are all defined in topology
and parameters
.
For nonbonded interactions, one can calculate all pair interactions (by setting rswitch
larger than rcutoff
) for non-periodic systems. However,sometimes it is computationally expensive to calculate all pair interactions. In this case (for both non-periodic and periodic systems), one can use a cutoff scheme to truncate the long-range interactions. In the cutoff scheme (electrostatic cutoff
), the interactions are truncated at a certain distance rcutoff
and a switching function is used to smoothly turn off the interactions at a distance of rswitch
. Such switching functions are different for Lennard-Jones and electrostatic interactions. The expressions are shown below:
The plots of these functions are shown below:

For periodic systems, one can use the particle mesh Ewald (PME) (electrostatic pme
) method to calculate long-range electrostatic interactions. Also, rcutoff
should be smaller than the half of periodic box size to avoid self interactions.
PSF File Format
A protein structure file (PSF) is a file format utilized to describe the topological information of biological macromolecules. PSF files primarily store information regarding atoms, bonds, angles, dihedral angles, and improper force terms. However, they do not contain atomic coordinates intrinsically.
The PSF file consists of the following sections related to Qbics:
Atoms: Lists the ID, residue information, atom type, charge, mass, etc. for each atom.
Bonds: Defines the covalent bonding connections. Each line contains the IDs of pairs of atoms.
Angles: Records bond angles formed by three atoms. Each row contains three sets of IDs.
Dihedrals: Defines dihedral (torsion) angles formed by four atoms. Each row contains four atomic IDs.
Impropers: Mechanical constraints used to maintain molecular planes (e.g., the coplanar structure of the benzene ring), four IDs per row.
1 6 !NTITLE
2REMARKS original generated structure x-plor psf file
3REMARKS 2 patches were applied to the molecule.
4REMARKS topology top_all27_prot_lipid.inp
5REMARKS segment U { first NTER; last CTER; auto angles dihedrals }
6REMARKS defaultpatch NTER U:1
7REMARKS defaultpatch CTER U:76
8
9 1231 !NATOM
10 1 U 1 MET N NH3 -0.300000 14.0070 0
11 2 U 1 MET HT1 HC 0.330000 1.0080 0
12 3 U 1 MET HT2 HC 0.330000 1.0080 0
13 4 U 1 MET HT3 HC 0.330000 1.0080 0
14 5 U 1 MET CA CT1 0.210000 12.0110 0
15 6 U 1 MET HA HB 0.100000 1.0080 0
16 7 U 1 MET CB CT2 -0.180000 12.0110 0
Key Sections of this file:
Title Section: Contains annotation information of the PSF file, such as generation method, topology file path, and so on.
- Atoms Section:
Atom ID: A unique number (e.g.
1
,2
).Segment Name: e.g.
U
for protein chain.Residue ID: The number of the residue to which the atom belongs (e.g.
1
for the first residue).Residue Name: e.g.
MET
for methionine.Atom Name: e.g.
N
,HT1
,HT2
,CA
for nitrogen, hydrogen, carbon, etc.Atom Type: The type used for force field calculations (e.g.
NH3
,HC
,CT1
).Charge: Partial charge of the atom (e.g.
-0.300000
).Mass: Mass of the atom (e.g.
14.0070
).
Then, the Bonds, Angles, Dihedrals, and Impropers sections follow, each containing the corresponding information. For example, the Bonds section contains the IDs of atoms that are bonded together:
1 7517 !NBOND: bonds
2 1 2 1 6 1 7 2 3
3 2 12 3 4 3 8 4 5
4 4 9 5 6 5 10 6 11
5 7 13 7 14 12 13 14 15
614 16 17 18 17 19 17 20
717 21 19 22 23 24 23 25
823 26 23 27 25 28 29 30
Here, we have bonds 1-2, 1-6, 1-7, 2-3, and so on. For others, the format is similar.
CHARMM Parameter File Format
CHARMM force field files define the rules and parameters of interactions between atoms in a molecular system. It contains several sections related to Qbics:
BONDS
: Describe the equilibrium lengths of covalent bonds and their corresponding force constants.ANGLES
: Provides the equilibrium value of the angle within the molecule and its force constant.DIHEDRALS
: Define the potential energy function and the corresponding parameters of the torsion angle.IMPROPERS
: Define the potential energy function and the corresponding parameters of the out-of-plane torsion angle.NONBONDED
: Define the Lennard-Jones potential.
Other sections like NBFIX
is NOT used by Qbics.
Input Examples
Example: Molecular Dynamics Simulation of Ubiquitin in Water
Below we provide an example of a Qbics input file for simulations of a protein “ubiquitin” in water. Below shows the system. It contains 24696 atoms, a ubiquitin in a 64x64x64 water box:

This system was built by randomly placing water molecules around the ubiquitin. This Usually leads to a high-energy system, and molecular dyanmics starting with this can be highly unstable. So, we first optimize it:
1charmm
2 # Here:
3 # toppar_water_ions.str: the parameter file for water and ions.
4 # par_all36m_prot.prm: the parameter file for proteins.
5 # Both are obtained from website: https://mackerell.umaryland.edu/charmm_ff.shtml.
6 parameters toppar_water_ions.str par_all36m_prot.prm
7 topology sys.psf
8 scaling14 1.0
9 rcutoff 12.0
10 rswitch 10.0
11 use_PBC # Add this line to turn on PBC.
12 Lbox 64 64 64 # Define the box size.
13 electrostatic pme # Use PME for electrostatics.
14 PMEk 64 64 64
15end
16
17opt
18 max_step 500
19end
20
21mol
22 sys.pdb
23end
24
25task
26 opt charmm
27end
After 500 steps, the energy decreased from 34167803.38107745 kcal/mol
to -82402.25839655 kcal/mol
.
Using the optimized structure, we can now perform a NVT MD simulation:
1charmm
2 # Here:
3 # toppar_water_ions.str: the parameter file for water and ions.
4 # par_all36m_prot.prm: the parameter file for proteins.
5 # Both are obtained from website: https://mackerell.umaryland.edu/charmm_ff.shtml.
6 parameters toppar_water_ions.str par_all36m_prot.prm
7 topology sys.psf
8 scaling14 1.0
9 rcutoff 12.0
10 rswitch 10.0
11 use_PBC # Add this line to turn on PBC.
12 Lbox 64 64 64 # Define the box size.
13 electrostatic pme # Use PME for electrostatics.
14 PMEk 64 64 64
15end
16
17md
18 type nvt
19 dt 0.001 # 1 fs
20 num_steps 1000 # 1 ps. Just for demonstration.
21 output_freq 100
22 temp 298
23end
24
25mol
26 charmm-1a-opt.xyz # Use the optimized structure from the previous step.
27end
28
29task
30 md charmm
31end