Dear Gromacs users, I have two queries : 1. I am doing simulation for a protein (156 residues ) with a sugar. Out of 156 protein resiudes i have restrained 130 residues and rest part i have kept free. My doubt is that when we can say that system has equilibrated?
if on the basis of rmsd then i dont feel it would be advisable to look the rmsd of protein because major part i have restrained, if i consider sugar rmsd then i can see a kind of periodicity in the rmsd. if i look the rmsd of the system then it seems to be stablized at 4.5nm. if i look the potential energy of the system then from the begining itself it seems to be equilibrated with a fluctuation of ~700kj/mol. I guess that may be because of very high contribution from the solvent. For nearly 26000 atoms i have done the simulation upto 4 ns. So i would just like to know that what is the best way to define system equilibration when a major part is restrained. 2. my second question is about caluclation of the interaction energy betwen the protein and the ligand. one possible way seems to be calculate all the energy pairs given by gromacs with ligand and protein (ljsr, ljlr, lj14 and for coulombs) and sum it or do i need to do two more simulations, one with protein alone in the same box size with same number of water molecules and other with the ligand alone and then substracting the sum of potential energies of independent simulations from the protein-ligand energy? any suggestion would be highly appreciated thanks _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
