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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><font size="3">Hi All,<br>
<br>
I have a question about periodic boundary conditions (pbc) when running a simulation to unfold a protein from its native structure.<br>
<br>
I set up pbc with the starting structure which is compact. <br>
When defining the box we use editconf and set up the -d 1.0 as the distance from the protein to the box edge.
<br>
It is said that "</font><font face="Arial" size="3">a protein should never see its periodic image".
<br>
If during the simulation the protein starts unfolding, the minimum distance from the protein to the box edge will no longer be 1.0 nm.
<br>
And it is possible that the length of the protein is even longer than the box dimension and the protein may "see" its periodic image in the neighbored box.<br>
Is this going to be a problem?<br>
I am also confused that it is also said that </font><font size="3">"(parts of) the molecule(s) diffuse out of the box is not a problem".<br>
Is this conflicted with </font><font size="3">"</font><font face="Arial" size="3">a protein should never see its periodic image"?</font><br>
<font size="3"><br>
Thank you.<br>
<br>
<br>
Best,<br>
<br>
Huilin</font><br>
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