Dear gmx-users, Greetings from Pawan. I have modelled the structure of a protein using Modeller and then energy minimized using gromacs. Then I used the popc128a bilayer from Tieleman sir's website for inserting the protein. I created a bigger bilayer using the genconf command in gromacs. I was able to minimize the bigger bilayer and then inserted my protein in the bilayer using the genbox command in gromacs. I was able to minimize the system. But when I tried to do an mdrun for few steps restraining the protein I ended with errors like : 1) pressure scaling more than 1% 2) Warning: 1-4 interaction between 1 and 8 at distance 1.6 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation. 3) too many lincs warnings. 4) Number of grid cells is zero. probably the system and the box collapsed.
I tried to solve these errors by increasing the tau_p value for pressure scaling error and higher table-extension value for the 1-4 interaction warning in the mdp file but nothing is working out. I have given the mdp files at the end for reference. Please give me some suggestions as how to continue further. For energy minimization: ------------------------------------ title = Protein in POPC bilayer cpp = /usr/bin/cpp define = -DFLEXIBLE integrator = steep nsteps = 50000 ; Constrain control constraints = none ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100 nstvout = 100 nstfout = 100 ; nblist update frequency nstlist = 10 ; ns algorithm ns_type = grid rlist = 1 ; Method for doing VdW vdw-type = Cut-off rvdw = 1 ; Method for doing electrostatics coulombtype = Cut-off rcoulomb = 1 ; Center of mass control nstcomm = 1 ; Periodic boundary conditions pbc = xyz ; Mode for center of mass motion removal comm-mode = Linear ; Energy minimizing stuff emtol = 2250 emstep = 0.001 For mdrun using position restraints: --------------------------------------------------- title = Protein in POPC cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 5000 ; total 10 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 Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-Protein ; Pressure coupling is not on Pcoupl = berendsen tau_p = 5.0 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 Pcoupl_type = semiisotropic ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Thanking you, Yours sincerely, Pawan
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