Hi Mark, Thanks for your reaction!
2018-03-12 18:08 GMT+01:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > On Mon, Mar 12, 2018 at 4:19 PM Douwe Pollmann <douwepollm...@gmail.com> > wrote: > > > 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. > > > > You should double check the documentation of the mdp options relevant to > these algorithms so that you know you are using them correctly - triangles > of constraints are more demanding than uncoupled ones. > I will play a bit more with the values for lincs-order and lincs-iter, or the value for shake-tol. > You should also make sure that your exclusions are appropriate. If the Cb > atom is having a non-bonded interaction with the Ca atoms (or their > neighbours) then you make life hard on the constraint implementation. > There is no interaction with the Cb's and the other atoms in the system, I excluded them all in the energygrp-excl. So unfortunately that isn't the solution.. > > > 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". > > > > No, SETTLE is specific to water, ie. molecules with three heavy atoms. > > > > 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. > > > > If you don't want constraints, don't ask for any :-) You also won't get > Yeah okay, true :) > your fixed triangle. You can of course do that, with due regard to your > timestep and validation of your module. > > 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? > > > > The ideal answer would be to use a virtual site in GROMACS, but there's no > way of constructing the Cb atom off the line of the two Ca atoms. There are > ways to construct the Cb atom on the line, or various ways from the > positions of three or more other atoms, but nothing is clearly suitable for > your case, unfortunately. > I also thought of virtual sites and I came to the same conclusion as you, so I was already afraid for this answer.. Thanks for thinking along! > > Mark > > 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. > > > -- > 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. > -- 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.