Hi All, I have been trying run energy minimization for a homoTRIMER protein, I have puzzled by the following results!
1) energy minimization in vacuum 1 chain is separated from the remaining 2 chains. I tried for 5 models in 4 models chains are separated and one is normal. 2)energy minimization in box with or with out solvent, no chain separation for all the 5 models. please note that EM method is steepest decent, I have tried size on the box up to 20nm. CONTESTS OF MDP FILE cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no What would be the probable reason for this. Please let me know. Regards Chandu _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
