> > Thank you Mark for your detailed explanation. Sorry if I am slow in >> understanding some stuff. I appreciate your patience. >> >> 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: >> >> [all chains] [all chains] >> >> [all chains] [all solvent] (group with all solvent atoms) >> >> [all solvent] [all solvent] >> >> (so [all chains] is consisting of atoms 1 to m + atom m+1 to 2m...) >> >> is there a way to get the same results by defining index groups as >> individual chains [chain 1] [chain 2] .. [chain n]? for example >> >> [chain 1] [all solvent] >> +[chain 2] all solvent] >> + chain 3 .. >> >> = ? [all chains] [all solvent] >> > > 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.
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: LJ SR of [chain 1] [chain 1]+ [chain 2] [chain 2]+ > [chain 3][chain 3]+ > .....= [all chains] [all chains] LJ SR > > 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? > > 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. >> > > What's the "usual sense" in which an energy of a binary mixture is > reported? > > > 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? >> > > What energy quantities are measured in "mol"? > > See http://www.mail-archive.com/[email protected]/msg27382.html for > discussion. > > 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. > 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? > 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)! >> > > 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. 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? > > > 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 >> [chain 1].... [chain n]? >> > > 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? 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]...) 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. :) > > > In other words [all chains] deals with all chains separately and reports >> quantities for ALL the chains as a group? >> > > 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. > 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. > 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] > ... > I thought in the case of interaction energies (question 1 above), gromcas looks at individual chains and adds up energies: [chain 1] [all solvent] +[chain 2] all solvent] + chain 3 .. = ? [all chains] [all solvent] Thank you for your time, > Mark > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Moeed Shahamat Graduate Student (Materials Modeling Research Group) McGill University- Department of Chemical Engineering Montreal, Quebec H3A 2B2, Canada Web: http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php Web:http://mmrg.chemeng.mcgill.ca/
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