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On 11/04/2012 1:24 AM, Shi, Huilin wrote:
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<div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0,
0); 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>
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<br>
Yes, if you don't allow for it from the start. Some test simulations
with implicit solvent are probably priceless here.<br>
<br>
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0); font-size: 10pt;"><font face="Arial" size="3">
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>
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</blockquote>
<br>
Sometimes - can depend on orientation of molecule wrt box.<br>
<br>
Mark<br>
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