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
--- On Tue, 3/9/10, Qiong Zhang<qiongzhang...@yahoo.com>
wrote:
From: Qiong Zhang
<qiongzhang...@yahoo.com>
Subject: Re:problem with interaction energy calculated by g_energy
To: gmx-users@gromacs.org
Date: Tuesday, March 9, 2010, 4:27 PM
Hi dear Mark,
Thanks very much for your reply.
Yes, you are right that I am using PME.
The molecules I am simulating are carbohydrates. And I am using Glycam06
Force Field.
The interaction energy I got previously is analyzed by directly using
g_energy, summing up Coul_SR and LJ_SR of two groups.
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.
Am I right here?
For the second summing up problem, I am still checking all the input file,
especially the index file.
Thank you very much!
Qiong
----- Original Message -----
From: Qiong Zhang<qiongzhang...@yahoo.com>
Date: Monday, March 8, 2010 20:35
Subject: [gmx-users] problem with interaction energy calculated by g_energy
To: gmx-users@gromacs.org
-----------------------------------------------------------
|> Dear gmx users,
>
> 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.
> 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?
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.
> 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
Coul_SR+LJ_SR.
> 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.
>
> Could anybody give me some hints or suggestions please?
They should add up. Check your index group definitions and use in the .mdp
file.
Mark
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