[gmx-users] Checking the possibility of one complex out of possible two

Pappu Kumar papuu_k at yahoo.com
Thu Mar 27 19:26:49 CET 2014

I got two long protein complexes made out of 20 monomers of ~300 residues. But only one complex exists biologically. I am trying to find out the energetically favourable complex by MD simulation in gromacs 4.6.5. Initially I took out a dimer from the complexes and ran steepest descent followed by L-BFGS minimization . Although the total energy was lower in one dimer, after the L-BFGS, the energy was similar. 

Then I ran 50ns MD simulation and calculated the interaction energies between the monomers which is similar in both cases. The idea was that in the wrong confomation the interaction energy would be lower. 

Now I am wondering how to find out the correct conformation between the two possibilites. I also checked the free energy of solvation which is different in both cases. I am not sure if it is a clear indicator of stability since entropy is not taken into account. Let me know if you have any ideas. I am planning to run coarse grained simulations in MARTINI.  Thank you.

More information about the gromacs.org_gmx-users mailing list