Dear justin In my work MD peptide(with 13 aa) I use this md.mdp.would ypu please say me Is that correct.
title = cpeptide MD cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 5000 ; total 5 ps. nstcomm = 1 nstxout = 50 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein sol ref_t = 300 300 ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 -- 2)In the place program doesent have phrase for example PME,....does. the gromacs use default? 3)when I use berendsen coupling is on and pcoup =yes and In my work is effect in fluctuate? best sh-karbalaee _______________________________________________ gmx-users mailing list [email protected] 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
