[gmx-users] Peptide out of box even after applying trjconv

Apramita Chand apramita.chand at gmail.com
Fri Jun 2 16:20:34 CEST 2017


Dear All,
 Even after applying g_trjconv -f file.gro -s file.tpr -pbc mol -ur compact
-center -o newfile.gro,
for visualisation purposes of peptide inside the box, a portion of it still
sticks out of the box. Is it unnatural?

What might be done to sort out the problem?

yours sincerely
Apramita


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