Re: [gmx-users] Pull parameters to Restrain motion along the Z Axis
suppose distance between center of masses of protein and DPPC is say 2.5 in the z direction and if pull_start =yes and pull_init is 1.0 then sampling will be at center of mass distance = 3.5 in only Z direction, since I have selected N N Y. That's correct. and if pull_start =No and pull_init is 1.0 then sampling will be done at center of mass distance = 1 in only Z direction. That's correct. Well,I am using that pull in each mdp file ( minimization, equilibration and Production). Is that a problem ? That's fine. It remains nearly at the similar distance as 0th frame throughout the simulations in Z direction. You may be near an energy barrier if you are sure that you have set the pull settings correctly, so you might have to increase the spring constant k in the pull code to get it exactly where you want it. I am sorry for the misunderstanding. I want to allow my protein only move in x, y direction. I am restricting it so It can't move be in Z direction. There might be other ways to do that with restraints, but this may give you the result you want, too. On Wed, Aug 26, 2015 at 8:38 PM, Barnett, James W jbarn...@tulane.edu wrote: pull_start = yes means COM distance is added to the pull_init value. So whatever distance your two pull groups starts out at plus pull_init is the window where it will sample. pull_start = no means just the pull_init value is used as the reference distance. If you have pull_init set to 1.0 then that is the reference distance for sampling (the window where it will sample). If you haven't equilibrated at the reference distance it could take a little bit for your two groups to get to the reference distance. At t=0 nothing has moved yet, unless you have equilibrated with the same pull code parameters already (and you probably should, depending on what your goal is here), so you should not expect the distance between the two groups to already be near the reference distance before the simulation has begun. If you're looking to restrain the protein's movement to the z-axis such that it can only move along the z-axis, this is not what you'll be achieving. Here are you restricting the movement of the protein along the z-axis but it is free to move in the x and y directions. I may be misunderstanding your goal here. There are some flat-bottom restraints you can add to make it such that the protein only moves in one direction if that's your goal. Check the relevant sections in the manual. -- James “Wes” Barnett, Ph.D. Candidate Louisiana Board of Regents Fellow Chemical and Biomolecular Engineering Tulane University 341-B Lindy Boggs Center for Energy and Biotechnology 6823 St. Charles Ave New Orleans, Louisiana 70118-5674 jbarn...@tulane.edu From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Live King vikasdubey1...@gmail.com Sent: Wednesday, August 26, 2015 5:25 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Pull parameters to Restrain motion along the Z Axis Hi, I use Gromacs 4.5.5. I have these pull parameters which I use to restrain my Protein motion along the Z axis.I want to make sure these parameters are fine or not since , I am not getting expected results. Also, please suggest any other parameters I can add. ;Pull to restrain Z position pull = umbrella pull_geometry= distance ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y pull_start = No pull_nstxout = 1 pull_nstfout = 1 pull_ngroups = 1 pull_group0 = DPPC pull_group1 = Protein pull_vec1= 0.0 0.0 0.0 pull_init1 = 1.0 pull_rate1 = 0 pull_k1 = 1000 pull_kB1 = 1000 Here I am completely confused in pull_init and pull_start. From my understanding, pull_init is the reference distance at t=0. The reference distance is the distance between COM of the pull group and COM of the reference group.I have set my reference group as DPPC and pull group as Protein, which means my Z_distance should be Ideally ~ 1.00 if my pull_start is set up as No and should be ~0.0 if that is set it as Yes.Since, pull_start means the initial COM distance is the reference distance for the first frame. But my values are instead after the production run:- with pull_init =1.0 and pull_start = Yes time |d| dx dy dz 0.0004.53616050.98503492.36917383.7407854 with pull_init =1.0 and pull_start= No 0.0002.82224150.78675102.5469491 -0.9268878
Re: [gmx-users] Pull parameters to Restrain motion along the Z Axis
Hi James, Thanks for your reply. I roughly got your point and still kinda confused. Please let me know If I am wrong . suppose distance between center of masses of protein and DPPC is say 2.5 in the z direction and if pull_start =yes and pull_init is 1.0 then sampling will be at center of mass distance = 3.5 in only Z direction, since I have selected N N Y. and if pull_start =No and pull_init is 1.0 then sampling will be done at center of mass distance = 1 in only Z direction. Well,I am using that pull in each mdp file ( minimization, equilibration and Production). Is that a problem ? It remains nearly at the similar distance as 0th frame throughout the simulations in Z direction. I am sorry for the misunderstanding. I want to allow my protein only move in x, y direction. I am restricting it so It can't move be in Z direction. Thanks, Vikas On Wed, Aug 26, 2015 at 8:38 PM, Barnett, James W jbarn...@tulane.edu wrote: pull_start = yes means COM distance is added to the pull_init value. So whatever distance your two pull groups starts out at plus pull_init is the window where it will sample. pull_start = no means just the pull_init value is used as the reference distance. If you have pull_init set to 1.0 then that is the reference distance for sampling (the window where it will sample). If you haven't equilibrated at the reference distance it could take a little bit for your two groups to get to the reference distance. At t=0 nothing has moved yet, unless you have equilibrated with the same pull code parameters already (and you probably should, depending on what your goal is here), so you should not expect the distance between the two groups to already be near the reference distance before the simulation has begun. If you're looking to restrain the protein's movement to the z-axis such that it can only move along the z-axis, this is not what you'll be achieving. Here are you restricting the movement of the protein along the z-axis but it is free to move in the x and y directions. I may be misunderstanding your goal here. There are some flat-bottom restraints you can add to make it such that the protein only moves in one direction if that's your goal. Check the relevant sections in the manual. -- James “Wes” Barnett, Ph.D. Candidate Louisiana Board of Regents Fellow Chemical and Biomolecular Engineering Tulane University 341-B Lindy Boggs Center for Energy and Biotechnology 6823 St. Charles Ave New Orleans, Louisiana 70118-5674 jbarn...@tulane.edu From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Live King vikasdubey1...@gmail.com Sent: Wednesday, August 26, 2015 5:25 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Pull parameters to Restrain motion along the Z Axis Hi, I use Gromacs 4.5.5. I have these pull parameters which I use to restrain my Protein motion along the Z axis.I want to make sure these parameters are fine or not since , I am not getting expected results. Also, please suggest any other parameters I can add. ;Pull to restrain Z position pull = umbrella pull_geometry= distance ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y pull_start = No pull_nstxout = 1 pull_nstfout = 1 pull_ngroups = 1 pull_group0 = DPPC pull_group1 = Protein pull_vec1= 0.0 0.0 0.0 pull_init1 = 1.0 pull_rate1 = 0 pull_k1 = 1000 pull_kB1 = 1000 Here I am completely confused in pull_init and pull_start. From my understanding, pull_init is the reference distance at t=0. The reference distance is the distance between COM of the pull group and COM of the reference group.I have set my reference group as DPPC and pull group as Protein, which means my Z_distance should be Ideally ~ 1.00 if my pull_start is set up as No and should be ~0.0 if that is set it as Yes.Since, pull_start means the initial COM distance is the reference distance for the first frame. But my values are instead after the production run:- with pull_init =1.0 and pull_start = Yes time |d| dx dy dz 0.0004.53616050.98503492.36917383.7407854 with pull_init =1.0 and pull_start= No 0.0002.82224150.78675102.5469491 -0.9268878 my protein is nearly at the center of membrane of box size 7.34147 7.34147 7.34147 If somebody can help me I will be grateful. Thanks, Vikas -- 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
Re: [gmx-users] Pull parameters to Restrain motion along the Z Axis
pull_start = yes means COM distance is added to the pull_init value. So whatever distance your two pull groups starts out at plus pull_init is the window where it will sample. pull_start = no means just the pull_init value is used as the reference distance. If you have pull_init set to 1.0 then that is the reference distance for sampling (the window where it will sample). If you haven't equilibrated at the reference distance it could take a little bit for your two groups to get to the reference distance. At t=0 nothing has moved yet, unless you have equilibrated with the same pull code parameters already (and you probably should, depending on what your goal is here), so you should not expect the distance between the two groups to already be near the reference distance before the simulation has begun. If you're looking to restrain the protein's movement to the z-axis such that it can only move along the z-axis, this is not what you'll be achieving. Here are you restricting the movement of the protein along the z-axis but it is free to move in the x and y directions. I may be misunderstanding your goal here. There are some flat-bottom restraints you can add to make it such that the protein only moves in one direction if that's your goal. Check the relevant sections in the manual. -- James “Wes” Barnett, Ph.D. Candidate Louisiana Board of Regents Fellow Chemical and Biomolecular Engineering Tulane University 341-B Lindy Boggs Center for Energy and Biotechnology 6823 St. Charles Ave New Orleans, Louisiana 70118-5674 jbarn...@tulane.edu From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Live King vikasdubey1...@gmail.com Sent: Wednesday, August 26, 2015 5:25 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Pull parameters to Restrain motion along the Z Axis Hi, I use Gromacs 4.5.5. I have these pull parameters which I use to restrain my Protein motion along the Z axis.I want to make sure these parameters are fine or not since , I am not getting expected results. Also, please suggest any other parameters I can add. ;Pull to restrain Z position pull = umbrella pull_geometry= distance ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y pull_start = No pull_nstxout = 1 pull_nstfout = 1 pull_ngroups = 1 pull_group0 = DPPC pull_group1 = Protein pull_vec1= 0.0 0.0 0.0 pull_init1 = 1.0 pull_rate1 = 0 pull_k1 = 1000 pull_kB1 = 1000 Here I am completely confused in pull_init and pull_start. From my understanding, pull_init is the reference distance at t=0. The reference distance is the distance between COM of the pull group and COM of the reference group.I have set my reference group as DPPC and pull group as Protein, which means my Z_distance should be Ideally ~ 1.00 if my pull_start is set up as No and should be ~0.0 if that is set it as Yes.Since, pull_start means the initial COM distance is the reference distance for the first frame. But my values are instead after the production run:- with pull_init =1.0 and pull_start = Yes time |d| dx dy dz 0.0004.53616050.98503492.36917383.7407854 with pull_init =1.0 and pull_start= No 0.0002.82224150.78675102.5469491 -0.9268878 my protein is nearly at the center of membrane of box size 7.34147 7.34147 7.34147 If somebody can help me I will be grateful. Thanks, Vikas -- 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.
