Re: [gmx-users] Atom positions change between topology generation and NVT equilibration
On 4/29/20 7:49 AM, Max Winokan wrote: My apologies for the missing images. Hopefully they are available along with the MDP in the following link: https://www.dropbox.com/sh/dnqz7c049f4tvw3/AAAGGZ8AF-ddQpBjD-QVf0OAa?dl=0 If anyone knows what could be going on, please let me know. Essentially the atom positions in the first NVT step are very different to the input topology, see my original email below. Was there an intervening energy minimization step? The output of pdb2gmx looks fine, though providing the actual coordinate files and topologies themselves would be more useful for diagnosing the issue. Note that if you are applying constraints, that operation is done before the first step so the coordinates can change. The distortion in the coordinates suggests and incorrect bonded topology. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Atom positions change between topology generation and NVT equilibration
Hi Max, In the .mdp file that you uploaded you are using constraints = h-bonds ; bonds involving H are constrained Is that the right file? Otherwise running without these constraints might help. On the off-chance that happened: not using -ignh in grompp avoids re-placement of hydrogens. Best, Christian On 2020-04-29 13:49, Max Winokan wrote: My apologies for the missing images. Hopefully they are available along with the MDP in the following link: https://www.dropbox.com/sh/dnqz7c049f4tvw3/AAAGGZ8AF-ddQpBjD-QVf0OAa?dl=0 If anyone knows what could be going on, please let me know. Essentially the atom positions in the first NVT step are very different to the input topology, see my original email below. Best, Max From: on behalf of Max Winokan Reply to: Date: Wednesday, 29 April 2020 at 1:36 PM To: Subject: [gmx-users] Atom positions change between topology generation and NVT equilibration Dear GMX-Users, I am running some simulations of unsolvated DNA base pair dimers, with a topology generated from a structure previously optimised with quantum mechanical models. Because these structures have been highly-optimised it is important that Gromacs begins the MD with these atom positions. After generating the topology with pdb2gmx I get the structure file (gc.gro) with the configuration seen below (after_pdb2gmx.jpg): This configuration matches the optimised input structure. However, when I examine the trajectory (.trr) produced by running my NVT simulation (the MDP file for which is attached), the first timestep is very different from the input gc.gro structure, as seen below (first_nvt_frame.jpg): The discrepancy is largest with the hydrogen atoms (which are not constrained of course), but all the atoms have been slightly shifted from the input configuration. Please could someone fill me in on the source of these position changes, and how I can modify my methods to avoid these. Thank you and best regards, Max Winokan PhD Candidate in Theoretical Physics Leverhulme Quantum Biology Doctoral Training Centre University of Surrey GU2 7XH Guildford United Kingdom Office: 03AZ04 Email: m.wino...@surrey.ac.uk -- 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] Atom positions change between topology generation and NVT equilibration
My apologies for the missing images. Hopefully they are available along with the MDP in the following link: https://www.dropbox.com/sh/dnqz7c049f4tvw3/AAAGGZ8AF-ddQpBjD-QVf0OAa?dl=0 If anyone knows what could be going on, please let me know. Essentially the atom positions in the first NVT step are very different to the input topology, see my original email below. Best, Max From: on behalf of Max Winokan Reply to: Date: Wednesday, 29 April 2020 at 1:36 PM To: Subject: [gmx-users] Atom positions change between topology generation and NVT equilibration Dear GMX-Users, I am running some simulations of unsolvated DNA base pair dimers, with a topology generated from a structure previously optimised with quantum mechanical models. Because these structures have been highly-optimised it is important that Gromacs begins the MD with these atom positions. After generating the topology with pdb2gmx I get the structure file (gc.gro) with the configuration seen below (after_pdb2gmx.jpg): This configuration matches the optimised input structure. However, when I examine the trajectory (.trr) produced by running my NVT simulation (the MDP file for which is attached), the first timestep is very different from the input gc.gro structure, as seen below (first_nvt_frame.jpg): The discrepancy is largest with the hydrogen atoms (which are not constrained of course), but all the atoms have been slightly shifted from the input configuration. Please could someone fill me in on the source of these position changes, and how I can modify my methods to avoid these. Thank you and best regards, Max Winokan PhD Candidate in Theoretical Physics Leverhulme Quantum Biology Doctoral Training Centre University of Surrey GU2 7XH Guildford United Kingdom Office: 03AZ04 Email: m.wino...@surrey.ac.uk -- 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.
