[gmx-users] index file groups

Nick joojoojooon at gmail.com
Fri Feb 25 08:37:29 CET 2011

Hello to all,

Please help me with the following questions. Your attention is greatly

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]

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. 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?

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)!

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]?

In other words [all chains] deals with all chains separately and reports
quantities for ALL the chains as a group?

Thank you,
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