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<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US">Hi dear Mark,<br>
<br>
Please ignor my last mail replied to you. I made some mistake there.<br>
<br>
Yes, you are right that I am using PME. The cutoff for the real space and
reciprocal space is 1.2nm.<br>
<br>
The molecules I am simulating are carbohydrates. And I am using Glycam06 Force
Field.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US">I tried there
different ways to calculate the interaction energy:<br>
<br>
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.<br>
The <a name="OLE_LINK2">interaction energy between 1 and 2 (E 1_2) =</a> E
Coul_SR + <st1:place w:st="on">E LJ_SR</st1:place> =-170.048+(-232.719)=<a name="OLE_LINK11">-402.767</a></span><span style=""><span style="font-size: 12pt;" lang="EN-US"> kJ/mol</span></span><span style=""></span><span style="font-size: 12pt;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US">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 + <st1:place w:st="on">E LJ_SR</st1:place>
=</span><span style="font-size: 12pt;" lang="EN-US"> </span><span style="font-size: 12pt;" lang="EN-US">-91.5234 + (-238.712) = <a name="OLE_LINK10">-330.235</a></span><span style=""><span style="font-size: 12pt;" lang="EN-US"> kJ/mol</span></span><span style=""></span><span style="font-size: 12pt;" lang="EN-US">, which is quite far from the previously -402.767</span><span style="font-size: 12pt;" lang="EN-US"> kJ/mol</span><span style="font-size: 12pt;" lang="EN-US">!!!! But this -330.235</span><span style="font-size: 12pt;" lang="EN-US"> 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. </span><span style="font-size: 12pt;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><b style=""><span style="font-size: 12pt;" lang="EN-US">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.<o:p></o:p></span></b></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US"><br>
The third approach, in order to include the long range interaction, I've also
tried<a name="OLE_LINK1"> "mdrun -rerun" option</a> 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:<br>
<br>
[Coul(SR+recip)+LJ(SR+Disper. corr.)]_3rd - [Coul(SR+recip)+LJ(SR+Disper.
corr.)]_2nd - [Coul(SR+recip)+LJ(SR+Disper. corr.)]_1<sup>st</sup><o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="IT">=Delta(Coul_SR)+<a name="OLE_LINK3">Delta(Coul_recip)</a>+Delta(LJ_SR)+<a name="OLE_LINK4">Delta(LJ_Disper.corr.)</a><o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US">=(</span><a name="OLE_LINK5"><span style="font-size: 12pt;" lang="EN-US">-128.73</span></a><span style="font-size: 12pt;" lang="EN-US">) + (-30.33) +(<a name="OLE_LINK7"> -252.021</a>) + <a name="OLE_LINK6">(-39.9</a>) = <span style="color: blue;">-450.217 </span>kJ/mol<span style="color: blue;"><o:p></o:p></span></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US">If we neglect the long-range interactions, namely, </span><span style="font-size: 12pt;" lang="EN-US">Delta(Coul_recip) and Delta(LJ_Disper.corr.),
we got the interaction energy </span><span style="font-size: 12pt;" lang="EN-US">-128.73
-252.021= <a name="OLE_LINK9">-380.751</a><a name="OLE_LINK8"><span style=""> kJ/mol</span></a>. We see here the long-range
contribution is not negligible. However, </span><span style="font-size: 12pt;" lang="EN-US">this short range energy </span><span style="font-size: 12pt;" lang="EN-US">-380.751 kJ/mol is neither close to the </span><span style="font-size: 12pt;" lang="EN-US">-330.235</span><span style="font-size: 12pt;" lang="EN-US"> kJ/mol nor </span><span style="font-size: 12pt;" lang="EN-US">-402.767</span><span style="font-size: 12pt;" lang="EN-US"> kJ/mol.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US">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?</span><span style="font-size: 12pt;" lang="EN-US"><br>
<br>
Thank you very much!<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt;" lang="EN-US">Qiong<br>
</span><span style="font-size: 12pt; font-family: 宋体;" lang="EN-US"> <br>
<br>
--- On <b>Tue, <st1:chsdate year="2010" month="3" day="9" islunardate="False" isrocdate="False" w:st="on">3/9/10</st1:chsdate>, Qiong Zhang <i><qiongzhang928@yahoo.com></i></b>
wrote:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom: 12pt; text-align: left;" align="left"><span style="font-size: 12pt; font-family: 宋体;" lang="EN-US"><br>
From: Qiong Zhang <qiongzhang928@yahoo.com><br>
Subject: Re:problem with interaction energy calculated by g_energy<br>
To: gmx-users@gromacs.org<br>
Date: Tuesday, March 9, 2010, 4:27 PM<o:p></o:p></span></p>
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<p class="MsoNormal" style="text-align: left;" align="left"><span style="font-size: 12pt; font-family: inherit;" lang="EN-US">Hi dear Mark,<br>
<br>
Thanks very much for your reply.<br>
<br>
Yes, you are right that I am using PME. <br>
<br>
The molecules I am simulating are carbohydrates. And I am using Glycam06
Force Field. <br>
<br>
The interaction energy I got previously is analyzed by directly using
g_energy, summing up Coul_SR and LJ_SR of two groups. <br>
<br>
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. <br>
Am I right here? <br>
<br>
For the second summing up problem, I am still checking all the input file,
especially the index file. <br>
<br>
Thank you very much!<br>
<br>
Qiong<br>
<br>
----- Original Message -----<br>
From: Qiong Zhang <<a href="http://us.mc538.mail.yahoo.com/mc/compose?to=qiongzhang928@yahoo.com" target="_blank">qiongzhang928@yahoo.com</a>><br>
Date: Monday, March 8, 2010 20:35<br>
Subject: [gmx-users] problem with interaction energy calculated by g_energy<br>
To: <a href="http://us.mc538.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<br>
-----------------------------------------------------------<br>
| > Dear gmx users,<br>
> <br>
> 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. <br>
> 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?<br>
<br>
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.<br>
<br>
> 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 <st1:place w:st="on">E D_2</st1:place>.
Still, these interaction energies are the sum of <br>
Coul_SR+LJ_SR.<br>
> 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. <br>
> <br>
> Could anybody give me some hints or suggestions please?<br>
<br>
They should add up. Check your index group definitions and use in the .mdp
file.<br>
<br>
Mark<o:p></o:p></span></p>
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