Dear gmx users, When I am minimizing a trimer protein in vacuum by SD as well as CG methods, one of the monomer gets apart from the rest of the protein and places itself away from the other two monomers, which are intact. No periodic box is assigned. But when I am running editconf and assigning a box, then the structures are intact. What is the reason for the above behaviour? I am pasting the em.mdp below:
cpp = /lib/cpp define = -DFLEX_SPC constraints = none ;integrator = CG integrator = steep nsteps = 1000 ; ; Energy minimizing stuff ; emtol = 100 ;for SD emstep = 0.1 ;for CG ;emstep = 0.001 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no Anwar ---------------------- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] ----------------------- - _______________________________________________ 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
