I have run a Molecular Dynamics Simulation and have a trajectory.. I have to calculate energy of only a small part of a protein for all conformations.. How to accurately calculate the energy of set of residues from whole protein? Is there any tool available?
Dear Jitesh! Try to create for Gromacs an index file with the specified region of the protein you need. Then run the molecular dynamics calculation by specifying in the parameters-file md.mdp the needed region for the parameter "energygrps".
Thank you so much.. I'll try this.. Can I do this for multiple such regions at one go?
Hi, which force field are you using ? Can you provide more details about this which will help in answering your question?
make_ndx -f protein_npt -o index.ndx
suppose u want to calculate GLU (200) LYS(300) interaction energy
resid 200
resid 300
it will include these residues in the index file.
Now go to the npt.mdp file include
energygroups = resid_200 resid_300
After running the simulation
g_energy -f protein_npt -o glu_tyr_int_eng
then select corresponding serial IDs
hope it helps.
@Jitesh: you can do that by incorporating the list of various residues in various sets. then you can run the g_energy script.
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