Dear all, I am simulating a protein containing 2 domains which are linked together by a loop of around 10 residues. When I am simulating the same in vacuum, after approx 1ns, the rmsd has increased from 5 angstroms to 25 angstroms with in 10 time steps. You can surely imagine how drastic the structural changes are happening. And also during the simulation after 500ps the protein started to rotate and later at approx 2ns the protein stopped rotation. What exactly might be happening there, why the protein is behaving like that. I am pasting the mdp file below. ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /lib/cpp constraints = all-bonds ;define = -DPOSRES integrator = md dt = 0.002 ; ps ! nsteps = 10000000 ; total 10000 ps. nstcomm = 1 nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 0.9 rcoulomb = 0.9 rvdw = 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = Protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp = 300.0 gen_seed = 173529
kindly guide me in this issue. regards 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
