[gmx-users] solvate with hexagonal box

Erik Marklund erik.marklund at kemi.uu.se
Mon Mar 27 13:54:04 CEST 2017

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 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>

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