[gmx-users] Problem with trjconv to keep molecule whole for multi-chain protein

[arrow50311]

Hi,

I recently got one problem with trjconv in order to keep protein whole
during post-simulation processing. The problem is my protein is a
multi-chain protein. I used dodecahedron for explicit solvent simulation.
When I use trjconv to process the data, the flag -pbc nojump -ur compact
will still leave part of the protein in its periodic image, and -pbc
molecule -ur compact will make each chain of the protein whole and in the
visualized box but sometimes cannot keep all chains together.

Could any experienced people know how to deal with that? Is there any way to
keep all chains together as in the native protein just to ensure a
continuous visualizing trajectory?

Thank you,



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