Hi I have done md simulation of a 2-domain protein in water, in 50 K but every time I did it these domains are separated from each other, and dont correct when I do trjconv -pbc nojump, previous time when I did em or pr by doing trjconv -pbc nojump, it corrected.
The 50.mdp file is: title = n.pdb cpp = /lib/cpp constraints = none integrator = md dt = 0.001 nsteps = 100000 constraint_algorithm = shake shake_tol = 0.0001 nstcomm = 1 comm_mode = Angular nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.4 0.4 tc-grps = protein non-protein ref_t = 50 50 ; Pressure coupling is on Pcoupl = berendsen tau_p = 2 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 50 K. gen_vel = yes gen_temp = 50.0 gen_seed = 173529 are they realy separated or I should do a command to correct it, I search in mailing list and could not find the result, please guide me, thank you in advance. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
