Hello,
I am solvating a short peptide with a dodecahedral box using the following GROMACS 4.6 commands:
pdb2gmx_mpi -ignh -f $1.pdb -o $1.gro -p $1.top -water spce -ff oplsaa
editconf_mpi -f $1.gro -o $1-BOX.gro -bt dodecahedron -d 2.5 -c
genbox_mpi -cp $1-BOX.gro -cs spc216.gro -p $1.top -o solv.gro
where $1 is the root name of my starting pdb
When I open solv.gro in Chimera or VMD I see a box that appears to be rectangular and the peptide is not in the center even though I used the -c flag in editconf.
I am wondering if this is normal or if I should do something differently with my setup.
Thanks!
A dodecahedral box is a more efficient one because it adds fewer waters to maintain the same periodic distance. This is merely a visualization inconvenience and there is no need to change the approach taken.
This is normal. The dodecahedron is re-wrapped within a triclinic representation. You can unwrap the PBC after you have created a .tpr file using trjconv -pbc mol -center but everything here looks fine.
A dodecahedral box is a more efficient one because it adds fewer waters to maintain the same periodic distance. This is merely a visualization inconvenience and there is no need to change the approach taken.
I experienced the same issue and here is the trick that worked for me.
The box has to be cubic + d 2.5 -c
See the full commands along with before and after in the image given below.
The image is only for non-commercial use and should not be used for any other means except educational purposes.
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