[gmx-users] solvate with hexagonal box

[Mark Abraham]

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.marklund at 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.marklund at kemi.uu.se<mailto:erik.marklund at 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-request at gromacs.org.