Dear gmx users,<br><br>Please kindly help me with the following issues:<br><br>I am trying to extract interaction energies (non bonded) between hexane molecules (vdw and electrostatics). I have used rerun program to exclude intramolecular non bonded terms and here is the breakdown of energy from g_energy. However, in the manual I read about dispersion correction and long range interactions. <br>
<br>Actually, I do not know for a hydrocarbon (hexane) system I should look at which contributions to get intermolecular interaction energies (long range, short range, dispersion correction) mainly because I can not distinguish them even after reding the maual<br>
<br>1- Can you please explain the difference between longe range and short range interactions. What this breakdown shows for intermolecular contributions is just short range LJ and coulomb (SR). Is there any other program (other than g_energy) to list other energy terms? <br>
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<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;">Energy<span style=""> </span>Average<span style=""> </span>RMSD<span style="">
</span>Fluct.<span style=""> </span>Drift<span style=""> </span>Tot-Drift</span></p>
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<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;">-------------------------------------------------------------------------------</span></p>
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<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;">Angle<span style=""> </span>4400.09<span style=""> </span>284.259<span style="">
</span>237.268<span style=""> </span>54.2184<span style=""> </span>542.293</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;">Ryckaert-Bell.<span style=""> </span>1009.62<span style=""> </span>124.468<span style="">
</span>94.0379<span style=""> </span>28.2417<span style=""> </span>282.474</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;">LJ-14<span style=""> </span>648.411<span style=""> </span>40.6844<span style="">
</span>39.926<span style=""> </span>2.70793<span style=""> </span>27.0848</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;">Coulomb-14<span style=""> </span>-278.654<span style=""> </span>34.4227<span style="">
</span>11.8071<span style=""> </span>11.1987<span style=""> </span>112.01</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;">LJ (SR)<span style=""> </span>-3010.16<span style=""> </span>47.968<span style="">
</span>42.5388<span style=""> </span>7.67736<span style=""> </span>76.789</span></p>
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<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;">Coulomb
(SR)<span style=""> </span>74.7846<span style=""> </span>2.5186<span style="">
</span>2.47007<span style=""> </span>0.170417<span style=""> </span>1.70451</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 9pt; font-family: Arial;">Coul.
recip.<span style=""> </span>-78.0436<span style=""> </span>2.58606<span style="">
</span>1.54725<span style=""> </span>-0.717662<span style=""> </span>-7.17805</span></p>
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<span style="font-size: 9pt; font-family: Arial;">Potential<span style=""> </span>2766.05<span style=""> </span>454.268<span style="">
</span>342.141<span style=""> </span>103.497<span style=""> </span>1035.18</span>
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2- In the manual I see the unit for energy is :KJ/mol but the unit for heat capacity obtained form g energy is in J/mol K. For this reason, I doubt the unit of energy in this list. Is it KJ/mol or J/mol? <br><br>3- I am trying to generate the top file for polyethylene chain using the information from the archive: <a href="http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html">http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html</a><br>
<br>What I intend to do is investigating the conformations of a much longer chain. Could you please tell me how to generate a longer chain with the given residue types proposed in the above post.<br><br><br>thank you,<br>
moeed<br><br> <input id="gwProxy" type="hidden"><input onclick="jsCall();" id="jsProxy" type="hidden"><div id="refHTML"></div>