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Hello, <br><br>I have an input structure with poor torsion angles and after minimization with gromacs (both steepest descent and congugate gradient) I found that they were not corrected. There is enough free space for the torsion angles to be corrected. <br>(I am sure of this because when I run the same structure in Insight it is able to correct them. Both programs give very similar structures with the major difference being the torsion angles.)<br><br>Has this happened because Gromacs potentials do not penalize poor omega angles? Or have I done something wrong? (I have added by .mdp file at the end of the mail)<br>Is there a way besides applying a restraint to every torsion angle to induce Gromacs to correct them? <br><br>Thank you in advance for you help,<br>Abdullah<br><br><br><br>; User spoel (236)<br>; Wed Nov 3 17:12:44 1993<br>; Input file<br>;<br>cpp = /usr/bin/cpp<br>define = -DPOSRES <br>constraints = none<br>integrator = cg<br>nsteps = 2000<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 2<br>emstep = 0.01<br><br>nstcomm = 1<br>ns_type = grid<br>rlist = 1<br>rcoulomb = 1<br>rvdw = 1<br>Tcoupl = no<br>Pcoupl = no<br>gen_vel = no<br><br>                                            </body>
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