[gmx-users] index file groups

[Mark Abraham]

On 25/02/2011 6:37 PM, Nick wrote:
> Hello to all,
>
> Please help me with the following questions. Your attention is greatly 
> appreciated.
>
> 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.

> 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.

> 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.

> 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?

> 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.

Mark