Hi Mark, Thanks. I will do so once my collaborators confirm that it’s ok that I upload the structure files.
Kind regards, Erik ______________________________________________ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 27 Mar 2017, at 20:20, Mark Abraham <mark.j.abra...@gmail.com<mailto:mark.j.abra...@gmail.com>> wrote: Hi, Sounds like there is something worth improving, although I can't answer your questions right now. Please open an issue on https://redmine.gromacs.org and attach a tarball of suitable inputs for the two(?) cases. Mark On Mon, 27 Mar 2017 13:54 Erik Marklund <erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>> wrote: Dear gmx-users, We are trying to merge a box containing a peripheral membrane protein with another box generated with memgen. Both boxes are hexagonal and exactly the same size,Naively, we thought that gmx solvate -cp protein.gro -cs membrane_and_water.gro would do the trick. Unfortunately, this causes gmx solvate to crash: Generating solvent configuration Will generate new solvent configuration of 1x2x1 boxes Solvent box contains 99373 atoms in 28208 residues Removed 12253 solvent atoms due to solvent-solvent overlap Removed 5122 solvent atoms due to solute-solvent overlap Sorting configuration Found 2 different molecule types: POPE ( 52 atoms): 233 residues SOL ( 3 atoms): 23294 residues gmx(16892,0x7fffaa24f3c0) malloc: *** error for object 0x7fe36d0008f0: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug Abort trap: 6 So we then tried to remove the membrane, keeping only the water, and use that system as the argument for -cs. Gmx solvate doesn’t crash now, but the output file has strange gaps of some size in the water parts, which cannot be explained by the removed lipids. Can gmx solvate not handle non-orthogonal boxes as arguments for -cs? The whole point in doing it this way was to avoid water molecules being inserted in the membrane. Perhaps overkill, but I am quite surprised at how bad things went with gmx solvate. Kind regards, Erik ______________________________________________ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se> -- 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<mailto: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<mailto: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.
