<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi dear Mark,<br><br>Thanks very much for your reply.<br><br>Yes, you are right that I am using PME. <br><br>The molecules I am simulating are carbohydrates. And I am using Glycam06 Force Field. <br><br>The interaction energy I got previously is analyzed by directly using g_energy, summing up Coul_SR and LJ_SR of two groups. <br><br>In order to include the long range interaction, I've also tried "mdrun -rerun" option. So three "reruns" were carried out for molecule 1(1st), molecules 2 (2nd) and molecule 1 and 2 (3rd). This time, I found the long range Coul_recip between molecule 1 and 2 is a quite positive value. So when only Coul_SR is included, the electrostatic interaction between molecule 1 and molecules 2 is much more negative (> 100 kj/mol) than that when both Coul_SR and Coul_recip are included. I guess, for such carbohydrate molecules, long
range Coul_recip can not be excluded. <br>Am I right here? <br><br>For the second summing up problem, I am still checking all the input file, especially the index file. <br><br>Thank you very much!<br><br>Qiong<br><br>----- Original Message -----<br>From: Qiong Zhang <<a ymailto="mailto:qiongzhang928@yahoo.com" href="http://us.mc538.mail.yahoo.com/mc/compose?to=qiongzhang928@yahoo.com">qiongzhang928@yahoo.com</a>><br>Date: Monday, March 8, 2010 20:35<br>Subject: [gmx-users] problem with interaction energy calculated by g_energy<br>To: <a ymailto="mailto:gmx-users@gromacs.org" href="http://us.mc538.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><br>-----------------------------------------------------------<br>| > Dear gmx users,<br>> <br>>
I am studying the adsorption behavior of a molecule ( molecule 1) on a
surface (molecules 2). Based on the production run, I calculated the
interaction energy between molecule 1 and molecules 2 by g_energy. <br>>
Here comes the first question: Why only short range interactions
between 1 and 2 are displayed, namely, Coul_SR and LJ_SR? So the
interaction energy E 1_2 I calculated is just the sum of Coul_SR+LJ_SR.
Will this bring about huge errors?<br><br>Guessing wildly (since you've
not told us the nature of your simulation protocol) you're using PME,
and so the long-range contributions cannot be decomposed group-wise.
This is probably a good thing - I'm not aware of any force field that
has been parameterized so that small chunks of atoms interaction
energies correlate to anything useful.<br><br>> After this, I'd like
to know the individual contributions of the components of molecule 1
to the interaction energy between 1 and 2. For example, molecule 1 is
composed of A, B, C and D resdues. So again, by g_energy, I got
interaction energy between A, B, C and D with 2, respectively, denoted
by E A_2, E B_2, E c_2 and E D_2. Still, these interaction energies are
the sum of <br> Coul_SR+LJ_SR.<br>> Then comes the second question:
Why the sum of E A_2, E B_2, E c_2 and E D_2 does not equal to E 1_2? I
found there was big difference between them, sometimes as large as 50
kJ/mol. <br>> <br>> Could anybody give me some hints or suggestions please?<br><br>They should add up. Check your index group definitions and use in the .mdp file.<br><br>Mark<br></td></tr></table><br>