Hi, I am trying to anneal two protein molecules. The usual protocol for a MD simulation was followed. But the problem arises that at high temperatures, the number of hydrogen bonds are increasing instead of getting decreased. The GROMOS43a1 force field was used and the mdp file for the simulation is shown below:
; title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ;ps ! nsteps = 5000000 ; total 10ns. ;nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Energy monitoring energygrps = Protein SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 2.75 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 310 K. gen_vel = no gen_temp = 300.0 gen_seed = 173529 ; SIMULATED ANNEALING CONTROL = annealing = periodic periodic annealing_npoints = 3 3 annealing_time = 0 5000 10000 0 5000 10000 annealing_temp = 300 500 300 300 500 300 Kindly help me as I am unable to figure out if there is a problem in my parameters file -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
