GROMACS version:2019
GROMACS modification: No
Hi all,
I would like for my molecule type-1 to only have repulsive interactions with my molecule type-2. In other words, how do I strip all the coulomb interactions and soft vdw interactions, while having hard core vdw interactions to account for excluded volume?
I have tried using the free energy options but I’m afraid that’ll strip interactions of moltype type-1 with all other molecules and not just with type-2.
Would appreciate any leads!
In GROMACS it is not possible to exclude Coulomb interactions between two molecule types. The only way to do this is to put both molecules in the same moleculetype, add exclusions for all inter-molecular atom pairs and add pair interactions between all inter-molecular atom pairs with only C12 set.
Thank you so much for your reply Hess!
I am trying to essentially figure out a way to get my co-solute (salt) and protein to only have excluded volume interactions. I need to do this to account for excluded volume interactions for my radial distribution functions. I have managed to figure out a way in which I can switch off coulombic and modulate vdw interactions using free energy options. It has some disadvantage since it also means that the vdw interactions between protein and water is also modulated. How does this sound to you , and also would you know of a way to essentially only have hard-core repulsions in my vdw term?
Highly appreciate your help!
free_energy = yes
init_lambda_state = 1
delta_lambda = 0
couple-moltype = Protein_chain_A
couple-lambda0 = vdw ; Only Vdw interactions (hopefully)
couple-lambda1 = none ; No interactions
couple-intramol = yes ; I’d like to have no intramolecular interactions as well
sc-alpha = 0.5
sc-coul = no
sc-power = 1
sc-sigma = 0.3
;nstdhdl = 1000
;init_lambda_state 0 1 2
vdw_lambdas = 0 0.9 1
coul_lambdas = 0 0 0
restraint_lambdas = 0 0 0
bonded_lambdas = 0 0 0
mass_lambdas = 0 0 0
temperature_lambdas = 0 0 0
I don’t see how it can be useful when the protein and the water do not interact.
What is your goal with this calculation?
I have radial distribution functions with my unbiased “normal” simulations and I see signatures of excluded volume in those rdfs. My goal is to construct a prior with excluded volume and to construct true rdf using that prior. Hence, I am looking to see if there’s a way to carry out simulations with excluded volume interactions between protein and salt.