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. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
