Vmd topotools free#

The output data file ( dump.lammpstrj) is loaded on to VMD using the GUI interface (see figure).

The visualisation of above described output data of LAMMPS is described in this section. This project then in turn demonstrates use of VMD to visualize the data set generated by LAMMPS from free-energy calculation of methane in water. The Python script, fep.py can be used to calculate the free-energy differences (T=300 K)ДЇep.py 300 < fep01.lmp fep.py 300 < fep10.lmp VMD Visualization The free-energy profiles can be observed by plotting the values in the third column of the results files ( fep01.lmp and fep10.lmp). LAMMPS generates output files fep01.lmp and fep10.lmp. This project has two LAMMPS input files (see the 'Files' tab): in_fep01.lmp and in_fep10.lmp. The atom coordinates from the simulation are dumped periodically on to an output file ( dump.lammpstrj).ДЇree energy perturbation is the difference between two calculations. The system is thermostatted at 300 K and barostatted at 1 atm, and time-integration is performed using the SHAKE algorithm.

An all-atom model of methane is allowed to interact with TIP4P model of water, and the interaction energy is modified as the coupling parameter О» is varied from 1 to 0.

Vmd topotools free#

The free energy of interaction between methane in a water solvent is calculated using the free-energy perturbation (FEP) method in LAMMPS.