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<DIV style="FONT: 9pt ËÎÌå">----- Original Message -----
<DIV style="BACKGROUND: #e4e4e4; font-color: black"><B>From:</B> <A
title=zhaolf@sjtu.edu.cn href="mailto:zhaolf@sjtu.edu.cn">Zhao Lifeng</A> </DIV>
<DIV><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV><B>Sent:</B> Friday, May 12, 2006 6:47 PM</DIV>
<DIV><B>Subject:</B> About calculations of viscosity</DIV></DIV>
<DIV><BR></DIV>
<DIV><FONT size=2>Dear gmx-users,</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2>I'm sorry to send the mail abruptly. I had emailed this
message to <A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> days
before, but there was no reply. Thank you very much for your kindly reading this
email and I expect your as kind instructions.</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US style="FONT-SIZE: 10pt; mso-font-kerning: 0pt"><FONT
face="Times New Roman">I¡¯m a new GMX user. I notice from either the user-manual
or the references (Palmer, PRE 49 359, & B. Hess, JCP 116, 209, etc.) that
there seem to be at least 3 methods available in Gromacs: Einstein relation,
TCAF and periodic perturbation method. But I¡¯m not very clear about how to set
the calculations and how to get the according viscosity
values.<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US style="FONT-SIZE: 10pt; mso-font-kerning: 0pt"><FONT
face="Times New Roman">My understanding is this:<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US style="FONT-SIZE: 10pt; mso-font-kerning: 0pt"><FONT
face="Times New Roman">For Einstein relation calculations, there is no special
setting in the md.mdp file, and the viscosity value is gotten by the visco.xvg
file generated by ¡®g_energy ¨Cvis¡¯; <o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US style="FONT-SIZE: 10pt; mso-font-kerning: 0pt"><FONT
face="Times New Roman">For TCAF, also there is no special setting in the md.mdp
file, and the viscosity value is gotten by fitting the data of visco_k.xvg file
generated by ¡®g_tcaf¡¯;<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US style="FONT-SIZE: 10pt; mso-font-kerning: 0pt"><FONT
face="Times New Roman">For the periodic perturbation method, two NEMD items, a
¡®accelerate¡¯ value in X direction should be specified to all atoms and a
¡®cos_acceleration¡¯ value should be given, and the viscosity value is gotten from
the ¡®1/Viscosity(SI)¡¯ item of the ¡®g_energy¡¯
results.<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US style="FONT-SIZE: 10pt; mso-font-kerning: 0pt"><FONT
face="Times New Roman">I¡¯m eager for any instructions about techniques on the
calculations and the value ranges. <o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US style="FONT-SIZE: 10pt; mso-font-kerning: 0pt"><FONT
face="Times New Roman">Thanks.</FONT></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US style="FONT-SIZE: 10pt; mso-font-kerning: 0pt"><FONT
face="Times New Roman"></FONT></SPAN> </P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US style="FONT-SIZE: 10pt; mso-font-kerning: 0pt"><FONT
face="Times New Roman">Lifeng Zhao</FONT></SPAN></P></FONT></DIV></BODY></HTML>