[gmx-users] trjconv centre protein

[Ewaru]

Hi,

I know this question has been asked for a few times already but I don't seem
to get it. :(
I did:

1) editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt dodecahedron 
2) genbox -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top
3) grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

and then I view the solv.gro file in VMD and found out that the protein is
hanging out from the box as in the attached image:

http://postimage.org/image/6df12u991/

I tried to put it in the centre with the command:

4) trjconv -s ions.tpr -f solv.gro -o solvcentre.gro -pbc mol -ur compact

But it shows that the protein (solvcentre.gro) is still the same (hanging
out from the box). Did I overlook something? Can I proceed with EM?

Please advice. :(

Thanking you in advance!

Best regards





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