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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">So if I wanna run a simulation to unfold the protein, I need make a big box that is large enough so that the unfolded protein is still smaller than the box in any dimension. Is
this correct?<br>
<br>
Thanks.<br>
<br>
Huilin<br>
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<div style="direction: ltr;" id="divRpF54275"><font color="#000000" face="Tahoma" size="2"><b>From:</b> gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of Mark Abraham [Mark.Abraham@anu.edu.au]<br>
<b>Sent:</b> Tuesday, April 10, 2012 11:54 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] protein folding / pbc<br>
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<div>On 11/04/2012 1:24 AM, Shi, Huilin wrote:
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<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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<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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<br>
Sometimes - can depend on orientation of molecule wrt box.<br>
<br>
Mark<br>
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