[gmx-users] editconf

Paymon Pirzadeh ppirzade at ucalgary.ca
Mon Oct 18 23:11:39 CEST 2010

I am trying to rotate my protein in my simulation box (solvent molecules
are there as well). I issue the following command:
 editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15
180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328

I select my group (protein) in the first group selection prompt and
whole system as output in the second prompt. However, in the output file
the whole system is rotated rather than protein only. Also, despite the
-box switch used, the dimensions of the box changes.
Is there any ideas on what I am missing in my procedure?


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