Re: [gmx-users] Nonsymetric molecule across pbc
On 2/18/14, 4:04 PM, Steven Neumann wrote: Or maybe just 2 of them in the box: so that the one in the cell and another one has its quarter in the unit cell edge and the free energy between them? Then this PMF take into account all of the others being copied around. Would US mdp option wont complain? Worth a try. This is a very complicated case that I doubt the pull code in Gromacs will deal with very elegantly. You can easily define two vectors along which to pull (one tube is pull_group0 and the other two are pull_group1 and pull_group2, with relevant vectors for the biasing restraint). That's a fairly simple 2-D PMF that can be done. The problem is in maintaining the equilateral geometry that you desire. To do that, you have to introduce a third restraint, which also somehow has to be debiased during WHAM. The problem is it does not come from the pull code, so I honestly don't know how to deal with it within Gromacs. You'll probably have to look into Alan Grossfield's WHAM program or something else entirely, like PLUMED. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Nonsymetric molecule across pbc
Thank you Justin. Indeed, the problem lies in maintaining the geometry... I need to simplify the system for free energy calculations. Steven On Wed, Feb 19, 2014 at 1:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/18/14, 4:04 PM, Steven Neumann wrote: Or maybe just 2 of them in the box: so that the one in the cell and another one has its quarter in the unit cell edge and the free energy between them? Then this PMF take into account all of the others being copied around. Would US mdp option wont complain? Worth a try. This is a very complicated case that I doubt the pull code in Gromacs will deal with very elegantly. You can easily define two vectors along which to pull (one tube is pull_group0 and the other two are pull_group1 and pull_group2, with relevant vectors for the biasing restraint). That's a fairly simple 2-D PMF that can be done. The problem is in maintaining the equilateral geometry that you desire. To do that, you have to introduce a third restraint, which also somehow has to be debiased during WHAM. The problem is it does not come from the pull code, so I honestly don't know how to deal with it within Gromacs. You'll probably have to look into Alan Grossfield's WHAM program or something else entirely, like PLUMED. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Nonsymetric molecule across pbc
Thanks a lot! Can you please give me a hint how to apply umbrella sampling to the system of 4 nanotubes with pbc across xyz so that they infinite in length in z coordinate and 2 of them placed with its half to the unit cell copied across y coordinate... I want to see PMF minima (equilibrium distance) between their centre of mass... With 2 nanotubes that would be easy (your tutorial) but with 4 of them? I am thinking of changing the distance between and run windows but no clue which group setup as group0 and group1... I would appreciate your advise, Steven On Tue, Feb 18, 2014 at 5:00 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/18/14, 11:19 AM, Steven Neumann wrote: Dear User, Can you please write me how to build a system of a protein (nonsymetric obviously) and place it in the on the box edge so that one half is within the unit cell and another one is copied across pbc on the other side? I assume I will get the error doing manually... Assuming box vectors of length x, y, z: editconf -center x/2 y/2 z will split the molecule across the boundary in the positive z-dimension. I can't think of a situation where this serves any useful purpose that centering does not, but that's how you'd do it. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Nonsymetric molecule across pbc
On 2/18/14, 1:37 PM, Steven Neumann wrote: Thanks a lot! Can you please give me a hint how to apply umbrella sampling to the system of 4 nanotubes with pbc across xyz so that they infinite in length in z coordinate and 2 of them placed with its half to the unit cell copied across y coordinate... I want to see PMF minima (equilibrium distance) between their centre of mass... With 2 nanotubes that would be easy (your tutorial) but with 4 of them? I am thinking of changing the distance between and run windows but no clue which group setup as group0 and group1... It's not clear what your objective really is, and I'm sorry to say that I find your description to be very confusing. A picture would help. What is your reaction coordinate? Are you trying to determine the free energy profile for one tube in relation to another, with 2 others as bystanders, or do the other 2 serve some functional role? If you're looking to do a multidimensional WHAM, you'll have to approach each reaction coordinate individually. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Nonsymetric molecule across pbc
Or maybe just 2 of them in the box: so that the one in the cell and another one has its quarter in the unit cell edge and the free energy between them? Then this PMF take into account all of the others being copied around. Would US mdp option wont complain? Steven On Tue, Feb 18, 2014 at 7:49 PM, Steven Neumann s.neuman...@gmail.comwrote: And the picture can be found here: http://speedy.sh/b73WM/Ssytem.png On Tue, Feb 18, 2014 at 7:49 PM, Steven Neumann s.neuman...@gmail.comwrote: Thanks, The picture is confidential so I will send it to you in the separate msg. The distance between all tubes e.g. is 10 nm at the picture (I will attach polypeptides to them later on). So I want to run window at this distance... Then decrease it every 0.2 nm so all distances will decrease between them...(3 tubes COM makes always isosceles traingle). I need to pull all of them somehow closer to each other with some constraints or distance restrarints I think...to reaach 9.8 nm etc. So I wish that the reaction coordinate would be the distance between all of their surfaces. Do you know what I mean? Or maybe build something easier...they all matter and will have influence on the distance... hence no clue which one of them apply with harmonic potential... Steven On Tue, Feb 18, 2014 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/18/14, 1:37 PM, Steven Neumann wrote: Thanks a lot! Can you please give me a hint how to apply umbrella sampling to the system of 4 nanotubes with pbc across xyz so that they infinite in length in z coordinate and 2 of them placed with its half to the unit cell copied across y coordinate... I want to see PMF minima (equilibrium distance) between their centre of mass... With 2 nanotubes that would be easy (your tutorial) but with 4 of them? I am thinking of changing the distance between and run windows but no clue which group setup as group0 and group1... It's not clear what your objective really is, and I'm sorry to say that I find your description to be very confusing. A picture would help. What is your reaction coordinate? Are you trying to determine the free energy profile for one tube in relation to another, with 2 others as bystanders, or do the other 2 serve some functional role? If you're looking to do a multidimensional WHAM, you'll have to approach each reaction coordinate individually. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
