[gmx-users] index file groups

Moeed lecielll at googlemail.com
Fri Feb 25 17:09:28 CET 2011

> 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/gmx-users@gromacs.org/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
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Moeed Shahamat
Graduate Student (Materials Modeling Research Group)
McGill University- Department of Chemical Engineering
Montreal, Quebec H3A 2B2, Canada
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