Re: [gmx-users] On the box type
Hi Cyrus, In a rectangular box (which is a specific case of a triclinic box) your molecule can't rotate freely without significant chance to run into its periodic image, invalidating whatever result you get. So, unless rotation is of no concern, or can be cirrcumvented, you'll need to use a rhombic dodecahedron. Cheers, Tsjerk On Sun, Jul 7, 2013 at 11:25 AM, akcyrus akcy...@gmail.com wrote: Dear all, I am planing to do pulling on a bundle of elongated proteins. I compared two box types - triclinic and dodecahedron. The volume and total number of atoms (protein+solvent), following the editconf and genbox commands, were 522.06 nm3 and 47921 for triclinic box and 2444.19 nm3 and 24 for dodecahedron. Although dodecahedron box has always been suggested due to shortcomings in the periodic interactions for a triclinic box, but I have seen examples of the use of triclinic box. Due to this huge difference in the number of solvents in the two cases I am tempted to use triclinic box, but I am a bit confused. Any ideas or suggestions? regards, cyrus -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] On the box type
Dear all and Tsjerk Wassenar, I could not grasp how a rectangular box will be a problem. Lets assume a I have a cylinder of radius r (nm) and height h (nm) with hr. I place the cylinder aligned along z-axis and then in a rectangular box with dimension 2r+2.0 nm, 2r+2.0 nm and 2h+2.0 nm. My understanding is that the problem could be when during simulation, the cylinder gets aligned parallel to XY plane and the box vectors are shorter along X and Y,isn't that right? Also during the simulation, with isotropic pressure coupling the box tend to be cubic and this would also cause problems. Correct me if I am wrong or don't understand it right. regards, akcyrus On Sun, Jul 7, 2013 at 12:00 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Cyrus, In a rectangular box (which is a specific case of a triclinic box) your molecule can't rotate freely without significant chance to run into its periodic image, invalidating whatever result you get. So, unless rotation is of no concern, or can be cirrcumvented, you'll need to use a rhombic dodecahedron. Cheers, Tsjerk On Sun, Jul 7, 2013 at 11:25 AM, akcyrus akcy...@gmail.com wrote: Dear all, I am planing to do pulling on a bundle of elongated proteins. I compared two box types - triclinic and dodecahedron. The volume and total number of atoms (protein+solvent), following the editconf and genbox commands, were 522.06 nm3 and 47921 for triclinic box and 2444.19 nm3 and 24 for dodecahedron. Although dodecahedron box has always been suggested due to shortcomings in the periodic interactions for a triclinic box, but I have seen examples of the use of triclinic box. Due to this huge difference in the number of solvents in the two cases I am tempted to use triclinic box, but I am a bit confused. Any ideas or suggestions? regards, cyrus -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] On the box type
On Sun, Jul 7, 2013 at 4:15 PM, akcyrus akcy...@gmail.com wrote: Dear all and Tsjerk Wassenar, I could not grasp how a rectangular box will be a problem. Lets assume a I have a cylinder of radius r (nm) and height h (nm) with hr. I place the cylinder aligned along z-axis and then in a rectangular box with dimension 2r+2.0 nm, 2r+2.0 nm and 2h+2.0 nm. My understanding is that the problem could be when during simulation, the cylinder gets aligned parallel to XY plane and the box vectors are shorter along X and Y,isn't that right? Yes. If that can happen, then your simulation will become junk when it does. Also during the simulation, with isotropic pressure coupling the box tend to be cubic and this would also cause problems. Correct me if I am wrong or don't understand it right. Anisotropic coupling is available. But I don't think that is an issue in choosing whether a rectangular box is plausible. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] On the box type
Dear all, The only tutorial on umbrella sampling by Justin ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html) assumes a rectangular box and pulling is done to separate chains. Is it true that the approach worked solely because one of the reference chains was position restrained as that did not allow it to rotate. regards, cyrus On Sun, Jul 7, 2013 at 4:45 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Sun, Jul 7, 2013 at 4:15 PM, akcyrus akcy...@gmail.com wrote: Dear all and Tsjerk Wassenar, I could not grasp how a rectangular box will be a problem. Lets assume a I have a cylinder of radius r (nm) and height h (nm) with hr. I place the cylinder aligned along z-axis and then in a rectangular box with dimension 2r+2.0 nm, 2r+2.0 nm and 2h+2.0 nm. My understanding is that the problem could be when during simulation, the cylinder gets aligned parallel to XY plane and the box vectors are shorter along X and Y,isn't that right? Yes. If that can happen, then your simulation will become junk when it does. Also during the simulation, with isotropic pressure coupling the box tend to be cubic and this would also cause problems. Correct me if I am wrong or don't understand it right. Anisotropic coupling is available. But I don't think that is an issue in choosing whether a rectangular box is plausible. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] On the box type
On 7/7/13 11:00 AM, akcyrus wrote: Dear all, The only tutorial on umbrella sampling by Justin ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html) assumes a rectangular box and pulling is done to separate chains. Is it true that the approach worked solely because one of the reference chains was position restrained as that did not allow it to rotate. Yes, the restraints prevent rotation while simultaneously serving other purposes (explained in the tutorial and associated paper). Please note that I also did analysis to determine that no spurious interactions occurred across PBC for this system. Normally, one would not use a rectangular box for a non-restrained system, though you should not necessarily view restraints as some generalized solution for the rotation problem - the general solution is to use a box that reflects the rotational symmetry of the system. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with box-type after the extension of simulation
On Wed, Nov 18, 2009 at 9:29 PM, sukesh chandra gain suk...@atc.tcs.comwrote: Dear All, I started a protein simulation for 100ps with octahedron box. After completion of that run I visualized the protein at the centre of the octahedron box by using trjconv. Then I have extended the simulation for another 500 ps by using tpbconv. But now it is showing as cubic box when I see the result after using trajconv (additionally some part of the protein is out of the box). This could only be a visualization glitch. Try using trjconv options. amit I do not have any clue how the box type has been changed or where could I go wrong. Please comment. Thank you, Cheers, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
