i see. i reran the trajectory with reaction field electrostatics and that gave a more negative energy value which was closer to what i was expecting. <br><br>i guess the missing reciprocal space contributions explains this discrepancy.
<br><br>is there a way to get the full interaction energy with PME ? <br><br>thnx for the reply<br>-sandeep <br><br><br><br><div class="gmail_quote">On Nov 17, 2007 8:18 PM, Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au">
mark.abraham@anu.edu.au</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">> Hi All<br>><br>> I simulated a cubic box of 2180 TIP3P water molecules using gmx
3.3 and PME<br>> for 400 ps and extracted the interaction energy of a randomly picked<br>water<br>> molecule with rest of the system.<br>> Simulation was done at 298K and 1bar and usual procedure for generating<br>
a<br>> water box and equilibration were used.<br>><br>> Average interaction energy reported in the log file was<br>> Epot (kJ/mol) Coul-SR LJ-SR<br>> WAT-rest -8.13828e+01 1.21886e+01
<br>><br>> giving a total of -8.13828e+01 + 1.21886e+01 = -69.194 kJ/mol<br>><br>> Comparing with published numbers using other MD programs this should be<br>in<br>> the range of -81 +/- 1 kJ/mol
i.e. ~11 kJ/mol less.<br>><br>> any clues on origin of this discrepancy ? relevant .top , .mdp files<br>are<br>> below.<br><br></div>The PME algorithm does an approximation to the full periodic Coulomb<br>summation, but does so with a calculation in direct space, as above, and
<br>another in reciprocal space, where your energy groups are not meaningful.<br>So you're only getting the direct-space component of the interaction<br>energy.<br><br>Mark<br><br>_______________________________________________
<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php
</a><br></blockquote></div><br>