GROMACS version:5
GROMACS modification: Yes/No
Hi gmx users,
I am trying to use gromacs in order to simulate proteins with a coarse grained c-alpha structure based model where the potential form is Go-like.
It is very easy to implement a pure repulsion for non-native non bonded interactions along with a 12-10 native contact potential.
But if I wish to change the non-native non-bonded interactions to LJ type(12-6 potential instead of earlier purely repulsive) along with a native contact potential as (12-10),Is there any way to tabulate the two kinds of potentials and use them (the type of equation potential energy has is like electrostatics +dispersion+repulsion, I would like to use two kind of dispersion instead of repulsion).
I know there is a way to do the same with different interactions by defining groups in index file for each type of residues and use multiple tabulated potential (As said in gromacs manual “Specifying the form for a particular inter-action”), but within an index group all atoms will interact with the same potential form (say 12-6 for non-native and 12-10 for native). But if we make an index group with all the contact residues, I don’t wish the 12-10 interaction between each of the contact residues as lets say 1-20 are in contact but 1 and every other residue in the native contact index group is not/may not be in contact. Right?
Is there any way to implement this?
Thanks in advance for your help,
Milan