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<pre>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.
<a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a>
><i> And I tried another way.
</i>><i> I change the content of .gro file.
</i>><i> I plus the number of residues in A-chain to B-chain's residue number.
</i>><i> And this new gro file shows the correct snapshot in VMD.
</i>><i> for example
</i>><i> my a-chain has 21 residues, b-chain has 30 residues.
</i>><i> In output .gro file the residue number is 1 to 21 and 1 to 30.
</i>><i>
</i>><i> I'm afraid VMD got confused for the repeat number 1 to 21.
</i>><i> So I change 1-30 in b-chain to 22-51.
</i>><i> Then snapshot in VMD become correct.
</i>
Then this was primarily VMD's issue.
-Justin</pre>
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Thank you for your help.<br>
I think I have no problem now.<br>
<br>
Hsin-Lin<br>
<br>
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