<table cellspacing='0' cellpadding='0' border='0' ><tr><td style="font: inherit;"><P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>Dear Sir,</FONT></P>
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<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3>I have found in literature that most of the unfolding studies of proteins are performed at higher temperature by increasing box size accordingly. My protein has approximately 70 residues, & I want to simulate it at room temperature as well as at some higher temperatures. I have not increased box size at higher temperatures in order to avoid computational cost, as right now we have some space problem. All my protein atoms are at a distance equal to 1.0 nm from the box edges at all temperatures. I have three queries.</FONT></P>
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<P class=MsoNormal style="MARGIN: 0in 0in 0pt 0.5in; TEXT-INDENT: -0.25in; TEXT-ALIGN: justify; mso-list: l0 level1 lfo1; tab-stops: list .5in"><FONT face="Times New Roman"><SPAN style="mso-list: Ignore"><FONT size=3>1)</FONT><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT size=3>Will the result be erroneous if I keep box size unaltered at higher temperature?</FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt 0.5in; TEXT-INDENT: -0.25in; TEXT-ALIGN: justify; mso-list: l0 level1 lfo1; tab-stops: list .5in"><FONT face="Times New Roman"><SPAN style="mso-list: Ignore"><FONT size=3>2)</FONT><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT size=3>What should be minimum distance between protein atoms and box edges? I have found that some authors say minimum distance will be 0.85 nm, but I also have found that several authors carried on simulations with dist 0.5nm between protein atoms and box edges, so I am getting confused.</FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt 0.5in; TEXT-INDENT: -0.25in; TEXT-ALIGN: justify; mso-list: l0 level1 lfo1; tab-stops: list .5in"><FONT face="Times New Roman"><SPAN style="mso-list: Ignore"><FONT size=3>3)</FONT><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT size=3>Is it sufficient to increase box size at higher temperature by 2/3 Å in all dimensions, how can I decide <SPAN style="mso-spacerun: yes"> </SPAN>increased dimension of the box at higher temperature? </FONT></FONT></P>
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<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>Please help.</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>Thanking you in advance.</FONT></P>
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<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>regards</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>Sangeeta</FONT></P><BR><BR>
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