No. You said before you had broken chains. Applying trjconv -pbc mol fixes
this issue. Molecules can be "broken" across periodic boundaries and is an
entirely normal phenomenon.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>/ And I tried another way.
/>/ I change the content of .gro file.
/>/ I plus the number of residues in A-chain to B-chain's residue number.
/>/ And this new gro file shows the correct snapshot in VMD.
/>/ for example
/>/ my a-chain has 21 residues, b-chain has 30 residues.
/>/ In output .gro file the residue number is 1 to 21 and 1 to 30.
/>/
/>/ I'm afraid VMD got confused for the repeat number 1 to 21.
/>/ So I change 1-30 in b-chain to 22-51.
/>/ Then snapshot in VMD become correct.
/
Then this was primarily VMD's issue.
-Justin
Thank you for your help.
I think I have no problem now.
Hsin-Lin
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