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<font class="Apple-style-span" face="Tahoma" size="2">Hello, </font><div style="font-family: Tahoma; font-size: 10pt; "><br></div><div style="font-family: Tahoma; font-size: 10pt; ">I would like to know if gromacs is designed to try and keep as close to the original structure as much as possible? </div><div style="font-family: Tahoma; font-size: 10pt; ">After minimizing a structure with phenyl-alanines I realized that a better minimization could be achieved if the rotamer had been changed during the minimization. However I have been unable to induce gromacs to do this on its own during minimization. </div><div style="font-family: Tahoma; font-size: 10pt; ">I could of course, change the original structure but I prefer not to. </div><div style="font-family: Tahoma; font-size: 10pt; "><br></div><div style="font-family: Tahoma; font-size: 10pt; ">Thank you in advance, </div><div style="font-family: Tahoma; font-size: 10pt; ">Abdullah Ahmed</div><div style="font-family: Tahoma; font-size: 10pt; "><br></div><div style="font-family: Tahoma; font-size: 10pt; ">My .mdp file is as follows: </div><div style="font-family: Tahoma; font-size: 10pt; "><br></div><div><div><font class="Apple-style-span" face="Tahoma" size="2">;</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">;<span class="Apple-tab-span" style="white-space:pre">        </span>User spoel (236)</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">;<span class="Apple-tab-span" style="white-space:pre">        </span>Wed Nov 3 17:12:44 1993</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">;<span class="Apple-tab-span" style="white-space:pre">        </span>Input file</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">;</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">;</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">cpp = /usr/bin/cpp</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">define = -DPOSRES </font></div><div><font class="Apple-style-span" face="Tahoma" size="2">constraints = none</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">integrator = steep</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">nsteps = 2000</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">;</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">; Energy minimizing stuff:</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">;</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">emtol = 0.2</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">emstep = 0.001</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"><br></font></div><div><font class="Apple-style-span" face="Tahoma" size="2">nstcomm = 1</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">ns_type = grid</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">rlist = 1</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">rcoulomb = 1</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">rvdw = 1</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">Tcoupl = no</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">Pcoupl = no</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">gen_vel = no</font></div></div>                                            </body>
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