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<DIV><FONT size=2>Hi,</FONT></DIV>
<DIV><FONT size=2> I use your algorithm to test.
The value is much different from </FONT></DIV>
<DIV><FONT size=2>g_energy's result.</FONT></DIV>
<DIV><FONT size=2> Your algorithm:
~10^5(KJ/mole * K)</FONT></DIV>
<DIV><FONT size=2> g_energy : ~ 10( J/mole *
K)</FONT></DIV>
<DIV><FONT size=2>I take a look about gmx source
code. There is one paraghaph about</FONT></DIV>
<DIV><FONT size=2>heat capacity. </FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2>VarT = RMSD(T) * RMSD(T), kb = 8.31451</FONT></DIV>
<DIV><FONT size=2>factor = nmol*ndf*VarT/(3.0*Temp*Temp)</FONT></DIV>
<DIV><FONT size=2>nmol = 1, ndf = 3</FONT></DIV>
<DIV><FONT size=2>Cv = kb / (2/3 - factor)</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2>It seems has no relationship with energy. I am
confused.</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2>Jia-lin </FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<BLOCKQUOTE dir=ltr
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt 新細明體">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt 新細明體; font-color: black"><B>From:</B>
<A title=ichorny@maxwell.compbio.ucsf.edu
href="mailto:ichorny@maxwell.compbio.ucsf.edu">Ilya Chorny</A> </DIV>
<DIV style="FONT: 10pt 新細明體"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt 新細明體"><B>Sent:</B> Wednesday, March 17, 2004 12:00
PM</DIV>
<DIV style="FONT: 10pt 新細明體"><B>Subject:</B> RE: [gmx-users] Calculate heat
capacity</DIV>
<DIV><BR></DIV>
<DIV><SPAN class=514142803-17032004><FONT face=Arial color=#0000ff size=2>The
heat capacity is proportional to the second moment (variance) of the
energy.</FONT></SPAN></DIV>
<DIV><SPAN class=514142803-17032004><FONT face=Arial color=#0000ff
size=2><sigma(E)^2> = k*T^2*Cv </FONT></SPAN></DIV>
<DIV><SPAN class=514142803-17032004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=514142803-17032004><FONT face=Arial color=#0000ff
size=2>Ilya</FONT></SPAN></DIV>
<DIV><SPAN class=514142803-17032004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> <A
href="mailto:gmx-users-admin@gromacs.org">gmx-users-admin@gromacs.org</A>
[mailto:gmx-users-admin@gromacs.org]<B>On Behalf Of </B>Jia-Lin
Lo<BR><B>Sent:</B> Tuesday, March 16, 2004 6:59 PM<BR><B>To:</B> <A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><B>Subject:</B>
[gmx-users] Calculate heat capacity<BR><BR></FONT></DIV>
<DIV><FONT size=2>Hi, </FONT></DIV>
<DIV><FONT size=2> I am doing a simple simulation (
protein in water). When I use </FONT></DIV>
<DIV><FONT size=2>g_energy to monitor the energy change, there are
several statistical values</FONT></DIV>
<DIV><FONT size=2>printed on screen. I notice the last line is the heat
capacity value. I would</FONT></DIV>
<DIV><FONT size=2>like to know how does it to be calculated? Is there
any formula for it ?</FONT></DIV>
<DIV><FONT size=2>I want to write a program to calculate it by myself.
</FONT></DIV>
<DIV><FONT size=2>Thanks for your help in advance.</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2>Jialin LO</FONT></DIV></BLOCKQUOTE></BLOCKQUOTE></BODY></HTML>