Re: [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?
Hi Mark, I use the Cb's to define a plane, and I use virtual sites to place beads in that plane. So the Cb's do not have non-bonded interactions with other beads, but they feel a force via the virtual sites. The problem is that my simulations are very unstable and that this is probably due to the fact LINCS and SHAKE have difficulties with the so called angle constraints. Douwe 2018-03-13 9:37 GMT+01:00 Mark Abraham : > Hi, > > If there's no interactions with CB then what's the point? > > Mark > > On Tue, Mar 13, 2018, 09:28 Douwe Pollmann > wrote: > > > Hi Mark, > > > > Thanks for your reaction! > > > > 2018-03-12 18:08 GMT+01:00 Mark Abraham : > > > > > 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.or
Re: [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?
Hi, If there's no interactions with CB then what's the point? Mark On Tue, Mar 13, 2018, 09:28 Douwe Pollmann wrote: > Hi Mark, > > Thanks for your reaction! > > 2018-03-12 18:08 GMT+01:00 Mark Abraham : > > > Hi, > > > > On Mon, Mar 12, 2018 at 4:19 PM Douwe Pollmann > > 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://mail
Re: [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?
Hi Mark, Thanks for your reaction! 2018-03-12 18:08 GMT+01:00 Mark Abraham : > Hi, > > On Mon, Mar 12, 2018 at 4:19 PM Douwe Pollmann > 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.
Re: [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?
Hi, On Mon, Mar 12, 2018 at 4:19 PM Douwe Pollmann 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. 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. > 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 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. 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.
