[gmx-users] Covalent bond/crosslink formation with calcium

[Turgay Cakmak]

Dear Gromacs users,


We are simulating a large nanofiber assembly composed of repeating units of
peptides, and we have been trying to see how the addition of calcium would
affect its behavior. We have already tried adding calcium ions in a random
distribution, which we successfully did.


But we also would like to insert calcium ions directly within the fiber
structure, near areas with negative charges that the calcium cation can
potentially bind. Is such a configuration possible (or sensible) to
simulate in Gromacs?


Likewise, we would like to specify a number of covalent bonds between some
of these side chains and the calcium ions, representing a well-crosslinked
system. Is this possible, and if so, do you know of a suitable set of
calcium forcefield parameters for the task?


Best regards, and thank you in advance for your assistance.


Turgay