Hello Dear users,<br><br>I appreciate your help with the following issues.<br><br> I am trying to extract interaction energies (non bonded) between hexane<br>
molecules (vdw and electrostatics). I have used rerun program to exclude<br>
intramolecular non bonded terms. In litrature people calculate these energies from vdw and electrostatics but <br>still I do not have a clear image on details of energy contributions. In GROMACS thre are good many options like SR, LR (PME/ dis correction).<br>
<br>1-Can you please guide me for my hydrocarbon system what would be the best approach to get interaction energies? below are the enrgy terms I have at the moment. Do I need to include disp. corrections as well?<br>Please help me with excluding or includeing PME and disp.corr contributions.<br>
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<p style="margin-bottom: 0cm;"><font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2">Energy
Average RMSD Fluct. Drift
Tot-Drift</font></font></p>
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</p>
<p style="margin-bottom: 0cm;"><font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2">------------------------------------------------------------------------------</font></font></p>
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<p style="margin-bottom: 0cm;"><font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2">Angle
4400.09 <br></font></font></p>
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</p>
<p style="margin-bottom: 0cm;"><font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2">Ryckaert-Bell.
1009.62 <br></font></font></p>
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</p>
<p style="margin-bottom: 0cm;"><font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2">LJ-14
648.411 <br></font></font></p>
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</p>
<p style="margin-bottom: 0cm;"><font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2">Coulomb-14
-278.654 <br></font></font></p>
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</p>
<p style="margin-bottom: 0cm;"><font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2">LJ
(SR) -3010.16 <br></font></font></p>
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</p>
<p style="margin-bottom: 0cm;"><font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2">Coulomb
(SR) 74.7846 <br></font></font></p>
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</p>
<p style="margin-bottom: 0cm;"><font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2">Coul.
recip. -78.0436 <br></font></font></p>
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</p>
<p style="margin-bottom: 0cm;"><font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2">Potential
2766.05 <br></font></font></p><br><br>
2- I have use nrexcl 7 in top file but I am still getting 1-4 interactions in breakdown! why is this heppening?<br><br>3- To calculate interaction energies can I sum up the energy contributions ? for example <br><p style="margin-bottom: 0cm;">
<font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2">LJ-14
648.411 + </font></font><font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2">Coulomb-14
-278.654 +LJ
(SR) -3010.16</font></font><font size="2"><font face="Arial, sans-serif"> </font></font>+Coulomb
(SR) 74.7846 =...</p><p style="margin-bottom: 0cm;"></p><p style="margin-bottom: 0cm;">4- About viewing the results: How can I plot the energy or force... vs. time ( graph)? I have found the program g_traj but it just lists the values ..no graph...!<br>
</p><font face="Arial, sans-serif"><font style="font-size: 9pt;" size="2"><br>Thank you for your time :)<br>MOeed<br><br></font></font>