Hi David,<br>
Its from one of the journal papers. Let me post what it said.<br>
----- This is what the paper says-----<br>
Alamethicin Helices in a Bilayer and in Solution: Molecular<br>
Dynamics Simulations<br>
D. Peter Tieleman,* Mark S. P. Sansom,# and Herman J. C. Berendsen*<br>
...................<br>
The pros and cons of this approach have <br>
been<br>
discussed by, e.g., Tobias et al. (1997). Water, lipid, and protein were<br>
coupled separately to a temperature bath at 300 K, with a coupling constant<br>
tT 5 0.1 ps. The velocities of the atoms were not scaled during the<br>
simulation. Although the use of separate temperature baths for different<br>
components of the system may be considered unphysical, it is necessary to<br>
avoid temperature gradients, and the parameters used have been chosen<br>
empirically to minimize the known drawbacks of this procedure.<br><br>
--------<br>
Thanks David.<br><div><span class="gmail_quote">On 1/19/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Viswanadham Sridhara wrote:<br>> Hi everyone,<br>><br>> I am reposting my earlier question, as I thought you might have missed it.<br>><br>> I am not quite able to understand the meaning of " The velocities of the
<br>> atoms were not scaled during the simulation". Then how can we use the<br>> temperature coupling?<br><br>Where does this message come from?<br><br>We need more info if you want answers to such questions. I have never
<br>seen this message before.<br><br><br>> Thanks,<br>> Vissu<br>><br>> On 1/18/06, *Viswanadham Sridhara* <<a href="mailto:muta.mestri@gmail.com">muta.mestri@gmail.com</a><br>> <mailto:<a href="mailto:muta.mestri@gmail.com">
muta.mestri@gmail.com</a>>> wrote:<br>><br>><br>> Hi everyone,<br>> I am not quite able to understand the meaning of " The velocities of<br>> the atoms were not scaled during the simulation". Then how can we
<br>> use the temperature coupling?<br>> Thanks,<br>> Vissu<br>> --<br>> Viswanadham Sridhara,<br>> Graduate Research Assistant,<br>> Old Dominion University, "VIRGINIA".
<br>><br>><br>><br>><br>> --<br>> Viswanadham Sridhara,<br>> Graduate Research Assistant,<br>> Old Dominion University, "VIRGINIA".<br>><br>><br>> ------------------------------------------------------------------------
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</a>.<br><br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
</a> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________<br>gmx-users mailing list
<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the
<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Graduate Research Assistant,<br>
Old Dominion University, "VIRGINIA".<br>