[gmx-users] Re:problem with interaction energy calculated by g_energy

[Qiong Zhang]

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




      
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