Hi dear Mark, Thank you very much for your reply!
Yes, you are right that I should have stated the gromacs version in my first mail. I am sorry that I did not notice this issue. I will pay attention to this next time. As for the electrostatic interaction energy in the long range, I am afraid that I have some different opinion which I am not sure if it is correct or not. I think for some systems with strong electrostatic interaction, for example, the interaction between a Rutile (TiO2) surface and a protein, it seems that the electrostatic interaction energy in the long range plays a very important role in the total interaction energy as one of my colleagues shows. In such cases, I think the electrostatic interaction energy in the long range can not be neglected. What is your opinion please? And I think I understand now "the reciprocal-space calculation cannot be decomposed group-wise." Maybe a better way to overcome this is using the formula: E_interact=E_tot(1-2)-E_tot(1)-E_tot(2) Do you agree with this? I am highly appreciative for all your help! Qiong On 9/03/2010 9:32 PM, Qiong Zhang wrote: Hi gmx users, 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: http://www.mail-archive.com/gmx-users@gromacs.org/msg20963.html 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. Well that's why we tell people to report their GROMACS version. :-) Using the latest version, and announcing what you are using can help you avoid wasting people's time :-) 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? Like I said last time, you can't do this with PME. The reciprocal-space calculation cannot be decomposed group-wise. Go read up on PME if you don't understand this. Also last time I pointed out this was a non-problem, for such an interaction energy doesn't mean much of anything anyway, even if you calculate it with some other electrostatics model. Mark [gmx-users] Re:problem with interaction energy calculated by g_energy Qiong Zhang Tue, 09 Mar 2010 01:17:02 -0800 Hi dear Mark, Please ignor my last mail replied to you. I made some mistake there. Yes, you are right that I am using PME. The cutoff for the real space and reciprocal space is 1.2nm. The molecules I am simulating are carbohydrates. And I am using Glycam06 Force Field. I tried there different ways to calculate the interaction energy: The first approach is analyzed by directly using g_energy, summing up Coul_SR and LJ_SR of two groups, since in the .mdp file I have defined in energygrps 1 2. The interaction energy between 1 and 2 (E 1_2) = E Coul_SR + E LJ_SR =-170.048+(-232.719)=-402.767 kJ/mol The second approach is using "mdrun -rerun" option with the exactly the same energygrps 1 2 defined in .mdp, the same traj.xtc and the same index. Weird enough, this time, I got interaction energy between 1 and 2 (E 1_2) = E Coul_SR + E LJ_SR = -91.5234 + (-238.712) = -330.235 kJ/mol, which is quite far from the previously -402.767 kJ/mol!!!! But this -330.235 kJ/mol is the exact sum of the contributions of subunits. The contributions of subunits are also calculated in this approach with rerun. So the discrepancy I reported in my first mail is solved. But what is the reason for the huge discrepancy between the interaction energy from the original run and the “rerun”?? I think they should be exactly the same. The third approach, in order to include the long range interaction, I've also tried "mdrun -rerun" option with three "reruns" carried out for molecule 1(1st), molecules 2 (2nd) and molecule 1 and 2 (3rd). The interaction energy for molecule 1 and 2 is now calculated by: [Coul(SR+recip)+LJ(SR+Disper. corr.)]_3rd - [Coul(SR+recip)+LJ(SR+Disper. corr.)]_2nd - [Coul(SR+recip)+LJ(SR+Disper. corr.)]_1st =Delta(Coul_SR)+Delta(Coul_recip)+Delta(LJ_SR)+Delta(LJ_Disper.corr.) =(-128.73) + (-30.33) +( -252.021) + (-39.9) = -450.217 kJ/mol If we neglect the long-range interactions, namely, Delta(Coul_recip) and Delta(LJ_Disper.corr.), we got the interaction energy -128.73 -252.021= -380.751 kJ/mol. We see here the long-range contribution is not negligible. However, this short range energy -380.751 kJ/mol is neither close to the -330.235 kJ/mol nor -402.767 kJ/mol. So Now I am confused. Which approach should be really adopted in the calculation of interaction energy? And what approach do you use in such interaction energy calculations? Thank you very much! Qiong
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php