I am trying to set up a molecular dynamics (GROMACS) simulation to study the effect of crowding agent on protein structure. I have referred several literature papers where they have mentioned modelling the crowding agent as a hard-core sphere but couldn't find relevant information to include spheres in the solvent. Can somebody please explain how to model and incorporate hard core spheres into the box along with the solvent and protein? Kindly let me know if any materials are available related to this work.
Hi,
This is an older conversation on the Gromacs mailing list: https://groups.google.com/forum/#!topic/archive-gmx-users/UZB-dHl5k7g
(if the link does not work, just search for "GROMACS hard spheres")
I hope it helps.
You can use tabulated potential. You can find the format for the tables in the manual
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