On 10/03/2010 7:56 AM, Qiong Zhang wrote:
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?
Important, yes - you need long-range electrostatics to sample the right
ensemble. Numerically meaningful when extracted from the whole
condensed-phase ensemble, no. If it's low, then the total energy has
sloshed into other degrees of freedom - so what? This is not gas-phase
ab initio quantum chemistry at 0K, where internal energy correlates with
something useful, because there are no other energetic degrees of
freedom. The frequency of occurrence of a region of structure space in a
converged trajectory can tell you something, i.e. relative free energies.
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?
No. The only term with long-range contributions is the reciprocal-space
term and it cannot be decomposed. There is no way around this.
If you can find a published article explaining the usefulness of the
analysis you're trying to do, they'll have used a forcefield and
electrostatics model that are consistent with doing it. You should copy
their method, in that case. I've given my advice three times, and am
going to desist :-)
Mark
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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