[gmx-users] solvate with hexagonal box

[Erik Marklund]

Done! https://redmine.gromacs.org/issues/2148

On 28 Mar 2017, at 10:24, Erik Marklund <erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>> wrote:

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.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se><mailto:erik.marklund at kemi.uu.se>

On 27 Mar 2017, at 20:20, Mark Abraham <mark.j.abraham at gmail.com<mailto:mark.j.abraham at gmail.com><mailto:mark.j.abraham at 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.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se><mailto: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><mailto:erik.marklund at kemi.uu.se><mailto:erik.marklund at kemi.uu.se>

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