[gmx-users] problem with pull code
Dear Sanku: I don't think that your setup is a particularly good idea. In addition to the potential for rotational problems that you mention, note that the pull force is going to be based on the shortest periodic distance between your group0 and group1. This can be across PBC in the Cartesian X dimension, and will be in your system unless your protein is 10 nm long. Also, you're going to have to present more information to get better assistance. Post your pull code parameters at the very least. Also, you say that your box dimensions are 20x8x8 nm, but your error message indicates a box dimension of 9 nm. Finally, that error message doesn't really make a lot of sense: Distance of pull group 1 (2.940209 nm) is larger than 0.49 times the box size (9.00) because 2.94 is less than 0.49*9, not greater as the error message states. I'm not sure if this is a gromacs error in an if statement or just a typo in the message that is output. I should add that you can do some of the testing yourself by using vacuum simulations and boxes of 20x8x8 and 20x20x20 and 50x50x50 (turn off PME for these tests and use the sd integrator) to see which ones give you a crash. Next time, please use a more informative title. Chris. -- original message -- I am trying to do an umbrella sampling of a fairly extended state of the protein along end-to-end distance of it. I am using a rectangular box ( elongated along x ) of dimension 20 nm X 8nm X 8 nm. I am doing the simulation in NVT ensemble. gromacs 4.5.4 is being used. But, even after running for 1 ns, the simulation crashes saying that Program mdrun_5mpi, VERSION 4.5.4 Source code file: pull.c, line: 329 Fatal error: Distance of pull group 1 (2.940209 nm) is larger than 0.49 times the box size (9.00) But if I see the trajectory, it hardly shows any issue with seeing the PBC image . I am not sure how to avoid this issue. Should I make one of the endgroup as freeze group so that it does not get tilted. Any help will be appreciated. Sanku -- 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] problem with pull code
Hi all, I am trying to do an umbrella sampling of a fairly extended state of the protein along end-to-end distance of it. I am using a rectangular box ( elongated along x ) of dimension 20 nm X 8nm X 8 nm. I am doing the simulation in NVT ensemble. gromacs 4.5.4 is being used. But, even after running for 1 ns, the simulation crashes saying that Program mdrun_5mpi, VERSION 4.5.4 Source code file: pull.c, line: 329 Fatal error: Distance of pull group 1 (2.940209 nm) is larger than 0.49 times the box size (9.00) But if I see the trajectory, it hardly shows any issue with seeing the PBC image . I am not sure how to avoid this issue. Should I make one of the endgroup as freeze group so that it does not get tilted. Any help will be appreciated. Sanku -- 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 pull code
On 10/13/12 3:17 PM, Sanku M wrote: Hi all, I am trying to do an umbrella sampling of a fairly extended state of the protein along end-to-end distance of it. I am using a rectangular box ( elongated along x ) of dimension 20 nm X 8nm X 8 nm. I am doing the simulation in NVT ensemble. gromacs 4.5.4 is being used. But, even after running for 1 ns, the simulation crashes saying that Program mdrun_5mpi, VERSION 4.5.4 Source code file: pull.c, line: 329 Fatal error: Distance of pull group 1 (2.940209 nm) is larger than 0.49 times the box size (9.00) But if I see the trajectory, it hardly shows any issue with seeing the PBC image . I am not sure how to avoid this issue. The pull code is very sensitive to these motions. Mathematically, I don't understand why mdrun is complaining, but your setup is prone to failure. An extended protein in an elongated box will surely interact with its periodic image at some point. Should I make one of the endgroup as freeze group so that it does not get tilted. I don't think you'll be able to freeze or restrain enough of the protein to make a difference that does not significantly impact the dynamics of the system. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
