[gmx-developers] Implicit solvent source code

Bernhardt, Nathan A. nbernhardt at ou.edu
Thu Oct 22 07:27:42 CEST 2015


I am performing simulations where i evolve 2 models (a go model and an all atom model using AMBER 99SB) independent of one another with the exception that they see each other through a potential which i have implemented. To do this, in GROMACS 4.6.5, i simply construct a topology using AMBER 99SB and add the atom types for the go model in my topology file. I then turn off long range interactions between the two using the “energygrp_excl” option in the mdp file. This works fine. The problem i have is as follows. i want to use an implicit solvent. The model handled by AMBER 99SB needs this treatment but the contact based go model does not. I add GBSA terms for the go model to my topology file, they are all zeros, and the simulation runs fine like this. However it is doing needless computations that results in zeros for the implicit model affect on the go model. I would like to have the source code skip these calculations for the go model, as this would speed up my simulations somewhat, but i can not find in the source code where these calculations are done. if anyone could point me in the right direction it would be most appreciated. 

Nathan Bernhardt

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