Hi,
The triclinic representation is used for all boxes in Gromacs as it is the
most compact. One needs to invoke trjconv with -pbc mol -ur compact to
obtain the expected visualization.
Well, it's not the most compact (otherwise -ur compact would yield you
a brick again), but it's the
try trjconv, maybe your reference gro/tpr file is cubic?
make sure:
trjconv -s the_dodecahedral_generated.tpr -f the_dodecahedral_generated.gro
-o your_aim.pdb
On Tue, May 22, 2012 at 9:27 AM, patrick wintrode pat_w...@yahoo.comwrote:
After generating my protein .gro and .top files and doing
On 5/22/12 6:36 PM, mu xiaojia wrote:
try trjconv, maybe your reference gro/tpr file is cubic?
make sure:
trjconv -s the_dodecahedral_generated.tpr -f the_dodecahedral_generated.gro -o
your_aim.pdb
The triclinic representation is used for all boxes in Gromacs as it is the most
compact.
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