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