Dear gmx users,
I want to measure the energy according to the conformation change of the ligand through free ligand simulation.
.1. Bond
.2. Angle
.3. Dihedral-proper
.4. Dihedral-improper
.27. Coulomb-14:LIG-LIG
.28. LJ-14:LIG-LIG
.25. Coulomb-SR:LIG-LIG
.26. LJ-SR:LIG-LIG
The sum of the above 8 terms was measured using gmx energy. Is this value representing the conformational energy of the ligand?
.8 Disper.-corr.
.10 Coul.-recip.
These two terms were not selected because they were considered to be values corresponding to the entire system rather than ligands due to long-range interaction. Is this correct?
I read the manual but it was too difficult for me. I’d appreciate it if you could explain it a little easier.
Kind regards,
Hi,
You did not specify the setting but I guess that you have a ligand in water+ion solution, you use PME to describe long range electrostatic and you use a force field that require DispersionCorrection.
Note, that not always energy decomposition is possible. For example if you use PME to describe the long you can not decompose the energy.
For example if you use PME to describe the long you can not decompose the energy.
well, you can decompose the energy, though its a bit involved … you need to do
a few re-reruns with modified topologies/tpr files …
one with all charges on the ligand set to zero, one with charges on all the rest set
to zero, and one with all charges on, take the difference and you get your electrostatic
contribution to the interaction (ligand-solvent) energy (VdW is easy, just use energy
groups). Then, another rerun with the ligand part of the trajectory only, and a suitable
tpr file, a cut-off that is longer than the longest extension of the ligand, and no PME -
this gives you the conformational energy of the ligand (bonded and intra-molecular
non-bonded) … for the dispersion correction you can perhaps use a similar
scheme, I didn’t think that through … also if the ligand carries a net-charge,
things are getting a bit more complicated … anything missing?
mic
