Dear all<br><br> After concatanation of protein with lipid I did inflatgro processing forscaling but I am facinng problem during energy minimisation step of inflatgro procedure . The minimisation terminated after few step and it converted into machine precision-<br>
Steepest Descents converged to machine precision in 349 steps,<br>but did not reach the requested Fmax < 1000.<br>Potential Energy = 4.2808670e+06<br>Maximum force = 4.9091840e+04 on atom 7290<br>Norm of force = 8.9087488e+02<br>
<br>As I searched its becoz of clashes between lipid and protein . <br>Do anyone have idea about how can we avoid these clashes ?whats the parameter required to avoid this?<br>the parameter file i am using is like this-<br>
cpp = /usr/bin/cpp<br>define = -DPOSRES<br>constraints = none<br>integrator = steep<br>nsteps = 10000<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 1000<br>
emstep = 0.001 <br><br>nstcomm = 1<br>ns_type = grid<br>rlist = 1<br>rcoulomb = 1.0<br>coulombtype = PME<br>rvdw = 1.0<br>Tcoupl = no<br>
Pcoupl = no<br>gen_vel = no<br>comm-mode = Linear<br>pbc = XYZ<br><br>SO please anyone suggest where I am doing fault ?<br><br>Nitu sharma<br>