Dear Gromacs users, I am currently working on a coarse-grained model where I want to fix atoms (Cb's) on a certain distance from Ca-Ca bonds, so that they can rotate freely. This freedom will be restricted by a dihedral that determines the relative orientation between the Cb's. I am using distance constraints or (non-chemical) bonds between a Cb and the adjacent Ca's, so that a fixed triangle is formed. I assumed that with this method the distance from Cb to the Ca-Ca bond should be correct and that my problem was solved. However, sometimes my simulations crash, and it appears that both constraint algorithms (LINCS and SHAKE) are not able to deal with angle constraints / 3 atoms bonded in a triangle.
I came up with two (maybe very strange) idea to solve this problem: 1: There is a third algorithm to solve constraints, called SETTLE, but it is stated almost everywhere that it is useful for water molecules. Do you know if it is possible to use SETTLE in other molecules than water, for example in my system? The Cb would be the "O", and the Ca's the "H's". 2: Is it possible to disable the constraint solver, so that neither Lincs and Shake are used? I am asking this because someone mentioned that the solvers are meant to reduce the very fast vibrations of light atoms, so that a larger mass on my Cb's will also solve the problem. For the method I want to use I really need the Cb's at fixed distances from the Ca's and the Ca-Ca bond, but I cannot think of any way without triangular constraints that fulfils these requirements. Does any of you know the answers to the two possible solutions, or a way to fix the distance between Cb and the Ca-Ca bond, while maintaining the free rotation? Thank you in advance for any help! Kind regards, Douwe Pollmann -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.