Dear Users ! I have done a minimization for a tetrapeptide in a water box
with conjugate gradient minimization of 1000 steps when I convert it to pdb as below ------------ trjconv -f em.trr -o min.pdb -s em.tpr << EOF 0 EOF -------------------- the out put pdb has many structures as follows MODEL 0 MODEL 1 MODEL 2 but the minimized pdb is single structre , what does these structures mean. how to obtain a single structre. my mimization input file is as follows -------------------------------------- define = -DFLEXIBLE constraints = none integrator = cg dt = 0.001 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 10.0 emstep = 0.01 energygrps = protein SOL ---------------------------------------- thanks in advance Dear Users ! I have done a minimization for a tetrapeptide in a water box with conjugate gradient minimization of 1000 steps when I convert it to pdb as below ------------ trjconv -f em.trr -o min.pdb -s em.tpr << EOF 0 EOF -------------------- the out put pdb has many structures as follows MODEL 0 MODEL 1 MODEL 2 but the minimized pdb is single structre , what does these structures mean. how to obtain a single structre. my mimization input file is as follows -------------------------------------- define = -DFLEXIBLE constraints = none integrator = cg dt = 0.001 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 10.0 emstep = 0.01 energygrps = protein SOL ---------------------------------------- thanks in advance
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