I performed MD simulations of an Ag-Ab complex. GROMACs treat the whole Ag-Ab complex as Protein in topology file. And I didn't provide index file which grouped Antigen and L-chain Ab and H-chain Ab for the MD run.
Is it possible to extract energy of just Antigen or L-chain or H-chain separately ?
Thanks
Dear Ajay,
You can form energy groups in your mdp file (keyword: energygrps), which should match with the groups in your index file. This will give you separate LJ and Coulomb interactions of each energy group with all energy groups. If you sum up the LJ and Coulomb interactions of desired groups (e.g. solvent-solvent or Ag-Ag etc.) this would ideally give you potential energies of each group.Hope this helps!
Dear Ajay,
if you stored your trajectory, you can calculate the energies for the different groups from it.
To do so, you can use the -rerun option of mdrun with which you provide your trajectory. For the rerun, use a tpr file generated with grompp from an mdp file (and corresponding index file) including those groups.
Best regards,
Martin
Dear Martin
Thanks a million for the help.
Just another query :
In Gromacs : Potential Energy is the addition of G96Bond, G96Angle, Proper-Dih, Improper-Dih, LJ-14, Coulomb-14, LJ-SR, LJ-LR, Coulomb-SR and Coulomb-LR.
And with gmx energy - I only get options of LJ and Coulomb energies for the defined energygrps in MDP : energygrps = a_1-1039 a_1040-3209 a_3210-5218
LJ-SR:a_1-1039-a_1-1039; etc
Is it there a way to get Potential / total energies of these groups (not binding energies) ? As I can get Kinetic from traj -ekt -ekr
Regards
Ajay
Have you stored velocities with your trajectory or only spatial coordinates?
Velocities are necessary to calculate the kinetic energy.
Dear Ajay,
You can form energy groups in your mdp file (keyword: energygrps), which should match with the groups in your index file. This will give you separate LJ and Coulomb interactions of each energy group with all energy groups. If you sum up the LJ and Coulomb interactions of desired groups (e.g. solvent-solvent or Ag-Ag etc.) this would ideally give you potential energies of each group.Hope this helps!
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