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] 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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