I want to perform MD Equilibration run under position restrained for 200ps. Bond distances were constrained using the LINCS (Linear Constraints) algorithm, the water molecules were restrained using the SETTLE algorithm. In order to do this I have modified nsteps in original pr.mdp file. Following is the modified file contents:
; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100000 ; total 200 ps. nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein SOL ; 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 Then I wanted to do grompp with this modified pr.mdp file. But it is showing a Fatal error like, Fatal Error: number of coordinates in coordinate file does not match topology. But if I use the original pr.mdp (without modifying it for 200ps) the grompp runs properly. I am not understanding what to do now. Please help me out. Thanking you, Chitrita.
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