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<div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thank you Mark for your detailed explanation. Sorry if I am slow in understanding some stuff. I appreciate your patience. <br>
<br>
1- I have an inquiry about index groups. If I specify all my solute chains as a whole in one group [all chains] (including n chains having m atoms each) and calculate interaction energies between the following:<br>
<br>
[all chains] [all chains]<br>
<br>
[all chains] [all solvent] (group with all solvent atoms)<br>
<br>
[all solvent] [all solvent]<br>
<br>
(so [all chains] is consisting of atoms 1 to m + atom m+1 to 2m...)<br>
<br>
is there a way to get the same results by defining index groups as individual chains [chain 1] [chain 2] .. [chain n]? for example<br>
<br>
[chain 1] [all solvent]<br>
+[chain 2] all solvent]<br>
+ chain 3 ..<br>
<br>
= ? [all chains] [all solvent]<br>
</blockquote>
<br></div>
Sure. GROMACS will let you define up to 256 energy groups. You just need to construct an appropriate index file. You can then add them together in whatever way suits you, but you'll need to use some other tool to post-process what g_energy reports.</blockquote>
<div><br> I think you answered my question here. If I understand correctly, say [all chains] [all chains] LJ-SR interaction energy is the sum of LJ SR with index file of separate chains. That is:<br>LJ SR of [chain 1] [chain 1]+<br>
[chain 2] [chain 2]+</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">[chain 3][chain 3]+</div></blockquote><div>.....= [all chains] [all chains] LJ SR <br>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"> <br>
In other words [all chains] looks at individual chains ([atoms 1 to m] + [atoms (m+1) to 2m] +...) but what it reports is sum over all individual chains?<br></div></blockquote><div><br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
2- The energy units are KJ per mol systems. I think this unit is not helpful since in literature what we see is energy of a quantity per mol in usual sense. <br>
</blockquote>
<br></div>
What's the "usual sense" in which an energy of a binary mixture is reported?<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
So my question is how can I get units in mol of particles for a binary mixture? on the list I read gromacs just divides energies by avogadros number...Does this mean there is no way of getting quantities in "mol" for mixtures?<br>
</blockquote>
<br></div>
What energy quantities are measured in "mol"?<br>
<br>
See <a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg27382.html" target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg27382.html</a> for discussion.<div class="im"><br>
Actually I was referring to the same post :) By "usual sense" I mean Avogadro number of particles. What I was trying to say is that, In literature we see thermodynamic quantities per mol (N_A particles). I dont think they report say heat of capacity per mole of systems..(what gromcs calculates). We always see experimental data in mole amount of substance.for pure systems, the values g_energy give should be divided by nmol (no of particles) to get values per mole of sunstnce and not system.</div>
</blockquote><div><br>For a binary mixture or ternary system, can we do the same thing by dividing by N_A? What I am interested in is interaction energies between my polymer and solvent. If I define my all chains as [all chains] and get LJ SR and coulomb SR for [all chains] [all chains], in order to ba able to compare this with those reported in literature, I need to divide by N_A?<br>
</div><div> <br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
3- If I run a simulation with one chain the interaction energy is smaller than a system with two chains..in fact there should be one specific value for interaction of component A with B independent of system size and number of particles. This is again a matter of units I think..How can I calculate the actual energies for a specific system so that they can be compared with those in literature (KJ/mol)!<br>
</blockquote>
<br></div>
Energies are dependent on system configuration and size. You have to make sure you are comparing like quantities, e.g. by normalizing with respect to the number of interacting chains, or atoms or whatever. I do not understand any sense in which your assertions above are true.</blockquote>
<div><br> Tsorry I was not clear with my question..As I mentioned just above, by normalizing you mean dividing by -nmol? If yes, for ternary system, I need to divide by N-A oly?<br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
4- Again regarding index groups, I am trying to realize how gromacs deals with a number of chains defined as awhole in a group [all chains]. For instance for Rg or end to end distance, what is calculated based on [all chains] is the average of the case with index file having<br>
[chain 1].... [chain n]?<br>
</blockquote>
<br></div>
You can calculate an end-to-end distance of a chain in a configuration. You can observe the average of that quantity over a set of configurations. You can compute that average over different sets of configurations, and average over those if you want to. But in what sense is the "end-to-end distance based on [all chains]" meaningful?</blockquote>
<div><br> By this question I was again trying to realize how calculations are done by specifying two different index files ( case 1: [all chains] and case 2: [chain 1] [chain 2]...)<br><br>As in question 1 above : for end to end distance does [all chains] looks at indivdual subchains and takes the average of Rg or End to end sidtance over chains or it looks at them as a whole group (a single longer chain containing atoms from atom number 1 to m*(chain number)..I think my question is clear now. :) <br>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
In other words [all chains] deals with all chains separately and reports quantities for ALL the chains as a group?<br>
</blockquote>
<br></div>
If you give a GROMACS tool a set of atoms over which to do an operation, it does that operation over that set of atoms. If that operation doesn't make sense on that set of atoms, then you've asked for a nonsense operation, and the problem does not lie with GROMACS. </blockquote>
<div> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">If you want the average of the end-to-end distance of all your chains over your simulation, then you'll have to compute the time-average for each chain individually, and then take the chain-average of them.<br>
</blockquote><div><br> I am sorry Mark but I still dont see this. From what you said here I understand that specifying [all chains] does not give average of the case with index file with [chain 1] [chain 2]</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
...<br></blockquote><div>I thought in the case of interaction energies (question 1 above), gromcas looks at individual chains and adds up energies:<br><br>[chain 1] [all solvent]<br>
+[chain 2] all solvent]<br>
+ chain 3 ..<br>
<br>
= ? [all chains] [all solvent]<br><br><br>Thank you for your time,<br> <br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Mark<br><font color="#888888">
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</font></blockquote></div><br><br clear="all"><br>-- <br>Moeed Shahamat<br>Graduate Student (Materials Modeling Research Group)<br>McGill University- Department of Chemical Engineering<br>Montreal, Quebec H3A 2B2, Canada<br>
Web:<a href="http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php">http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php</a><br>Web:<a href="http://mmrg.chemeng.mcgill.ca/">http://mmrg.chemeng.mcgill.ca/</a><br>