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<h1><font style="font-weight: normal;" size="2">Hi</font> <font size="2">gmx users, <br></font></h1>I found the big discrepancy between the interaction energy I got from my first approach and send approach should be ascribed to a bug reported here:<br><br>http://www.mail-archive.com/gmx-users@gromacs.org/msg20963.html<br><br>The gromacs I am using now is exactly gmx4.0.4. I also reran with a parallel version and the energies never changed during the rerun stage.<br><br>Still, the discrepancy in the energies between the second approach and the third approach is still puzzled to me. Which one is the correct way of calculating interaction energy?<br><br>Thank you very much!<br><br>Qiong<br><h1><font size="2"><span class="subject">[gmx-users] Re:problem with interaction energy calculated by g_energy</span></font></h1>
<p><span class="sender">Qiong Zhang</span><br>
<span class="date">Tue, 09 Mar 2010 01:17:02 -0800</span></p>
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<pre><br><br>Hi dear Mark,<br><br><br><br>Please ignor my last mail replied to you. I made some mistake there.<br><br><br><br>Yes, you are right that I am using PME. The cutoff for the real space and<br>reciprocal space is 1.2nm.<br><br><br><br>The molecules I am simulating are carbohydrates. And I am using Glycam06 Force<br>Field.<br><br> <br><br>I tried there<br>different ways to calculate the interaction energy:<br><br><br><br>The first approach is analyzed by directly using g_energy, summing up Coul_SR<br>and LJ_SR of two groups, since in the .mdp file I have defined in energygrps 1<br>2.<br><br>The interaction energy between 1 and 2 (E 1_2) = E<br>Coul_SR + E LJ_SR =-170.048+(-232.719)=-402.767 kJ/mol<br><br> <br><br>The second approach is<br>using "mdrun -rerun" option with the exactly the same energygrps 1 2 defined<br>in .mdp, the same traj.xtc and the same index. Weird enough, this time, I got <br>interaction<br>energy between 1 and 2
(E 1_2) = E Coul_SR + E LJ_SR<br>= -91.5234 + (-238.712) = -330.235 kJ/mol, which is quite far from the <br>previously -402.767 kJ/mol!!!! But this -330.235 kJ/mol is the exact sum of the<br>contributions of subunits. The contributions of subunits are also calculated in<br>this approach with rerun. So the discrepancy I reported in my first mail is<br>solved. <br><br> <br><br>But what is the reason for the huge discrepancy between<br>the interaction energy from the original run and the “rerun”?? I think they<br>should be exactly the same.<br><br><br><br>The third approach, in order to include the long range interaction, I've also<br>tried "mdrun -rerun" option with three<br>"reruns" carried out for molecule 1(1st), molecules 2 (2nd) and<br>molecule 1 and 2 (3rd). The interaction energy for molecule 1 and 2 is now<br>calculated by:<br><br><br><br>[Coul(SR+recip)+LJ(SR+Disper. corr.)]_3rd - [Coul(SR+recip)+LJ(SR+Disper.<br>corr.)]_2nd -
[Coul(SR+recip)+LJ(SR+Disper. corr.)]_1st<br><br>=Delta(Coul_SR)+Delta(Coul_recip)+Delta(LJ_SR)+Delta(LJ_Disper.corr.)<br><br>=(-128.73) + (-30.33) +( -252.021) + (-39.9) = -450.217 kJ/mol<br><br> <br><br>If we neglect the long-range interactions, namely, Delta(Coul_recip) and <br>Delta(LJ_Disper.corr.),<br>we got the interaction energy -128.73<br>-252.021= -380.751 kJ/mol. We see here the long-range<br>contribution is not negligible. However, this short range energy -380.751 <br>kJ/mol is neither close to the -330.235 kJ/mol nor -402.767 kJ/mol.<br><br> <br><br>So Now I am confused. Which approach should be really<br>adopted in the calculation of interaction energy? And what approach do you use<br>in such interaction energy calculations?<br><br><br><br>Thank you very much!<br><br> <br><br>Qiong<br><br> <br><br><br><br>--- On Tue, 3/9/10, Qiong Zhang <qiongzhang...@yahoo.com><br>wrote:<br><br><br><br>From: Qiong Zhang
<qiongzhang...@yahoo.com><br><br>Subject: Re:problem with interaction energy calculated by g_energy<br><br>To: gmx-users@gromacs.org<br><br>Date: Tuesday, March 9, 2010, 4:27 PM<br><br><br> <br> <br> Hi dear Mark,<br><br> <br><br> Thanks very much for your reply.<br><br> <br><br> Yes, you are right that I am using PME. <br><br> <br><br> The molecules I am simulating are carbohydrates. And I am using Glycam06<br> Force Field. <br><br> <br><br> The interaction energy I got previously is analyzed by directly using<br> g_energy, summing up Coul_SR and LJ_SR of two groups. <br><br> <br><br> In order to include the long range interaction, I've also tried "mdrun<br> -rerun" option. So three "reruns" were carried out for<br> molecule 1(1st), molecules 2 (2nd) and molecule 1 and 2 (3rd). This time, I<br> found the long range Coul_recip between molecule 1 and 2 is a quite positive<br> value. So when only Coul_SR is included, the
electrostatic interaction<br> between molecule 1 and molecules 2 is much more negative (> 100 kj/mol)<br> than that when both Coul_SR and Coul_recip are included. I guess, for such<br> carbohydrate molecules, long range Coul_recip can not be excluded. <br><br> Am I right here? <br><br> <br><br> For the second summing up problem, I am still checking all the input file,<br> especially the index file. <br><br> <br><br> Thank you very much!<br><br> <br><br> Qiong<br><br> <br><br> ----- Original Message -----<br><br> From: Qiong Zhang <qiongzhang...@yahoo.com><br><br> Date: Monday, March 8, 2010 20:35<br><br> Subject: [gmx-users] problem with interaction energy calculated by g_energy<br><br> To: gmx-users@gromacs.org<br><br> <br><br> -----------------------------------------------------------<br><br> | > Dear gmx users,<br><br> > <br><br> > I am studying the adsorption behavior of a molecule ( molecule 1) on a
<br>surface<br> (molecules 2). Based on the production run, I calculated the interaction<br> energy between molecule 1 and molecules 2 by g_energy. <br><br> > Here comes the first question: Why only short range interactions between<br> 1 and 2 are displayed, namely, Coul_SR and LJ_SR? So the interaction energy E<br> 1_2 I calculated is just the sum of Coul_SR+LJ_SR. Will this bring about huge<br> errors?<br><br> <br><br> Guessing wildly (since you've not told us the nature of your simulation<br> protocol) you're using PME, and so the long-range contributions cannot be<br> decomposed group-wise. This is probably a good thing - I'm not aware of any<br> force field that has been parameterized so that small chunks of atoms<br> interaction energies correlate to anything useful.<br><br> <br><br> > After this, I'd like to know the individual contributions of the<br> components of molecule 1 to the interaction energy between 1 and 2.
For<br> example, molecule 1 is composed of A, B, C and D resdues. So again, by<br> g_energy, I got interaction energy between A, B, C and D with 2,<br> respectively, denoted by E A_2, E B_2, E c_2 and E D_2.<br> Still, these interaction energies are the sum of <br><br> Coul_SR+LJ_SR.<br><br> > Then comes the second question: Why the sum of E A_2, E B_2, E c_2 and E<br> D_2 does not equal to E 1_2? I found there was big difference between them,<br> sometimes as large as 50 kJ/mol. <br><br> > <br><br> > Could anybody give me some hints or suggestions please?<br><br> <br><br> They should add up. Check your index group definitions and use in the .mdp<br> file.<br><br> <br><br> Mark<br></pre></td></tr></table><br>