<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi gmx users,<br><br>Thanks Mark very much for all your suggestions, for your detailed explanation and your patience with me. :-)<br><br>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.<br><br>Any advice or comment are welcome!<br><br>Thank you very much in advance.<br><br>Qiong<br><br><pre style="margin: 0em;">On 10/03/2010 7:56 AM, Qiong Zhang wrote:<br></pre><blockquote style="border-left: 0.2em solid rgb(85, 85, 238); margin: 0em; padding-left: 0.85em;"><pre style="margin: 0em;">Hi dear Mark,<br><br>Thank you very much for your reply!<br><br>Yes, you are right that I should have stated the gromacs version in my first<br>mail. I am sorry that I did not notice this issue. I will pay attention<br>to this next time.<br><br>As for the electrostatic interaction energy in the long range, I<br>am afraid that I have some different opinion which I am not sure<br>if it is correct or not. I think for some systems with
strong<br>electrostatic interaction, for example, the interaction between a<br>Rutile (TiO2) surface and a protein, it seems that the electrostatic<br>interaction energy in the long range plays a very important role in<br>the total interaction energy as one of my colleagues shows. In such<br>cases, I think the electrostatic interaction energy in the long<br>range can not be neglected. What is your<br> opinion please?<br></pre></blockquote><tt>Important, yes - you need long-range electrostatics to sample the right
</tt><tt>ensemble. Numerically meaningful when extracted from the whole
</tt><tt>condensed-phase ensemble, no. If it's low, then the total energy has
</tt><tt>sloshed into other degrees of freedom - so what? This is not gas-phase
</tt><tt>ab initio quantum chemistry at 0K, where internal energy correlates with
</tt><tt>something useful, because there are no other energetic degrees of
</tt><tt>freedom. The frequency of occurrence of a region of structure space in a
</tt><tt>converged trajectory can tell you something, i.e. relative free energies.
</tt><blockquote style="border-left: 0.2em solid rgb(85, 85, 238); margin: 0em; padding-left: 0.85em;"><pre style="margin: 0em;">And I think I understand now"the reciprocal-space<br>calculation cannot be decomposed group-wise." Maybe a better way<br>to overcome this is using the formula:<br><br>E_interact=E_tot(1-2)-E_tot(1)-E_tot(2)<br><br>Do you agree with this?<br></pre></blockquote><tt>No. The only term with long-range contributions is the reciprocal-space
</tt><tt>term and it cannot be decomposed. There is no way around this.
</tt><tt>If you can find a published article explaining the usefulness of the
</tt><tt>analysis you're trying to do, they'll have used a forcefield and
</tt><tt>electrostatics model that are consistent with doing it. You should copy
</tt><tt>their method, in that case. I've given my advice three times, and am
</tt><tt>going to desist :-)
</tt><pre style="margin: 0em;">Mark<br><br></pre><br></td></tr></table><br>