[gmx-users] Protein goes out of the box

spss4 at iacs.res.in spss4 at iacs.res.in
Tue Apr 25 16:39:09 CEST 2017

Hii all,
I have simulated protein in 45% ethanol water mixture for 100ns. After
completion of the job I saw that maximum portion of my protein goes out of
the box. Then I have done trjconv -pbc mol to the trajectory file. After
trjconv some portion of the protein is still out of the box. I want to see
the local environment of the protein using the .gro file(last frame) but
some portion of protein is dry. How can I get the actual state of protein
after completion of 100ns?
Thanks in advance.

Sunipa Sarkar

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