fix tmd command¶
fix ID group-ID tmd rho_final file1 N file2
ID, group-ID are documented in fix command
tmd = style name of this fix command
rho_final = desired value of rho at the end of the run (distance units)
file1 = filename to read target structure from
N = dump TMD statistics every this many timesteps, 0 = no dump
file2 = filename to write TMD statistics to (only needed if N > 0)
fix 1 all nve fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file
Perform targeted molecular dynamics (TMD) on a group of atoms. A holonomic constraint is used to force the atoms to move towards (or away from) the target configuration. The parameter “rho” is monotonically decreased (or increased) from its initial value to rho_final at the end of the run.
Rho has distance units and is a measure of the root-mean-squared distance (RMSD) between the current configuration of the atoms in the group and the target coordinates listed in file1. Thus a value of rho_final = 0.0 means move the atoms all the way to the final structure during the course of the run.
The target file1 can be ASCII text or a gzipped text file (detected by a .gz suffix). The format of the target file1 is as follows:
0.0 25.0 xlo xhi 0.0 25.0 ylo yhi 0.0 25.0 zlo zhi 125 24.97311 1.69005 23.46956 0 0 -1 126 1.94691 2.79640 1.92799 1 0 0 127 0.15906 3.46099 0.79121 1 0 0 ...
The first 3 lines may or may not be needed, depending on the format of the atoms to follow. If image flags are included with the atoms, the first 3 lo/hi lines must appear in the file. If image flags are not included, the first 3 lines should not appear. The 3 lines contain the simulation box dimensions for the atom coordinates, in the same format as in a LAMMPS data file (see the read_data command).
The remaining lines each contain an atom ID and its target x,y,z coordinates. The atom lines (all or none of them) can optionally be followed by 3 integer values: nx,ny,nz. For periodic dimensions, they specify which image of the box the atom is considered to be in, i.e. a value of N (positive or negative) means add N times the box length to the coordinate to get the true value.
The atom lines can be listed in any order, but every atom in the group must be listed in the file. Atoms not in the fix group may also be listed; they will be ignored.
TMD statistics are written to file2 every N timesteps, unless N is specified as 0, which means no statistics.
The atoms in the fix tmd group should be integrated (via a fix nve, nvt, npt) along with other atoms in the system.
Restarts can be used with a fix tmd command. For example, imagine a 10000 timestep run with a rho_initial = 11 and a rho_final = 1. If a restart file was written after 2000 time steps, then the configuration in the file would have a rho value of 9. A new 8000 time step run could be performed with the same rho_final = 1 to complete the conformational change at the same transition rate. Note that for restarted runs, the name of the TMD statistics file should be changed to prevent it being overwritten.
Restart, fix_modify, output, run start/stop, minimize info¶
No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands.
This fix is not invoked during energy minimization.
This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS was built with that package. See the Build package page for more info.
All TMD fixes must be listed in the input script after all integrator fixes (nve, nvt, npt) are applied. This ensures that atoms are moved before their positions are corrected to comply with the constraint.
Atoms that have a TMD fix applied should not be part of a group to which a SHAKE fix is applied. This is because LAMMPS assumes there are not multiple competing holonomic constraints applied to the same atoms.
To read gzipped target files, you must compile LAMMPS with the -DLAMMPS_GZIP option. See the Build settings doc page for details.
(Schlitter1) Schlitter, Swegat, Mulders, “Distance-type reaction coordinates for modelling activated processes”, J Molecular Modeling, 7, 171-177 (2001).
(Schlitter2) Schlitter and Klahn, “The free energy of a reaction coordinate at multiple constraints: a concise formulation”, Molecular Physics, 101, 3439-3443 (2003).