[gmx-users] TOPIC: PROBLEM WITH CENTRING PROTEIN IN A BOX

[Vlad Scepanovsky]

Hi, Dear GROMACS Users,

I've got a problem with centring protein in a box.

While running 

editconf -f sys_b4editconf.gro -o sys_b4genbox.gro -bt octahedron -d 1.0 -c

I have centered my protein in a box, but while running all the rootines up to 

mdrun -s md.tpr -o md.trr -x md.xtc -c sys_b4mdend.gro -e md.edr -g md.log
-v   

I found that my protein came out of the box.

trgconv with the option -center was used but that did not resolve my problem.

trgconv -f first.gro -o last.gro -s md.tpr -center

Could you please help me with my problem?



 


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