Hi, I want to modify the contribution to Interaction energy of different groups - say I have groups A and B and I want the energy to be scaled as E_AA + 0.1E_AB + 0.5*E_BB. Interaction parameters of each of these groups are set by a forcefield
Now after multiple correspondence on the gromacs list I have concluded that there are 3 ways of doing this: 1. Using tables - for this I would have to list non-bonded parameters for all atoms such that the combination rule and the table-potential is used. For the table for BB interaction, scale the Coloumb and VdW interactions in the tables by a factor of 0.5 and so on... However, since tables would have to be supplied for pairs too (tablep), it may not be accurate to supply 6-12 tables with coulomb potential for these pairs. I am using CHARMM and the 1998 paper on CHARMM says that in some specific cases the 1-4 interactions many be scaled which makes me doubt this approach. 2. Forcefield parameters - By defining scaled [nonbonded_params] for all relevant atoms. This will change the VdW interactions, but not sure about the Coulomb interactions. 3. Modifying gromacs - by passing a parameter lambda to gromacs which scales the force/potential by a factor lambda when gromacs calculates force/potential. For implementing option 3, which programs in the gromacs package would be the bes tstarting points for editing the energy contributions of different groups/atoms? As a more general question, how does one run a generalized Hamiltonian REM on gromacs? Pooja -- Quaerendo Invenietis-Seek and you shall discover.
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