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

Qiong Zhang qiongzhang928 at yahoo.com
Wed Mar 10 10:46:54 CET 2010

Hi gmx users,

Thanks Mark very much for all your suggestions, for your detailed explanation and your patience with me. :-)

Actually, I am going to study the desorption free energy of molecule 1 from the surface of molecule 2. So first I have to carry out the absorption of molecule 1 onto surface of molecule 2. I have tried 8 different orientations of molecule 1 with respect to the surface and have to choose ONE orientation with the most stability to proceed. I think the best criteria to choose ONE orientation is to compare the interaction energy between molecule 1 and 2. You mentioned relative free energy. But it seems to me difficult to compare the relative free energy between different orientations.  I read some papers on the simulation of Protein on some surface simulated by NAMD, [for example, Biomaterials 29 (2008) 513–532] The approach they adopted is also to compare the interaction energy (E_inter = E_(1+2) - E_1 - E_2). They also used PME to deal with the long range electrostatic interaction. The force field they used is charmm.

Any advice or comment are welcome!

Thank you very much in advance.


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:


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 :-)

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