<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1">
<title></title>
</head>
<body text="#000000" bgcolor="#ffffff">
Thanks a lot for your answer.<br>
<br>
1. I run the simulations with the center of mass motion removal. Do I
miss the translational motions altogether?<br>
2. If the answer to my first question is true, does the different
between the two calculations described below, i.e. with and without
fit, correspond to the rotational contribution to the entropy?<br>
3. Can I calculate the overall entropy from the simulation?<br>
<br>
Ran.<br>
<br>
Nguyen Hoang Phuong wrote:<br>
<blockquote type="cite"
cite="midPine.LNX.4.44.0410281832330.17633-100000@marge.theochem.uni-frankfurt.de">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">I tried to calculate the quasi-harmonic entropies from an MD simulation
from the covariance matrix, using g_covar as follows:
(1). Using the -nofit flag
(2). After fitting the coordinates to the initial configuration
When examining the eigenvalues, I got 3N eigenvalues for (1) and 3N-6
for (2) - i.e. the last 6 values were several orders of magnitude
smaller than the eigenvalues just prior to them, and some were negative
(and still, very close to zero).
According to Andricioaei and Karplus (J Chem Phys 115: 6289), one needs
to use 3N-6 degrees of freedom in order to calculate the entropy in a
quasi-harmonic representation. Hence, my questions are:
1. Should I expect to find the difference in the number (and magnitude)
of eigenvalues in (1) and (2), or is there a problem with the accuracy
of the simulation?
2. Which eigenvalues should I use?
3. If I use the eigenvalues obtained from (2), do I account for all
degrees of freedom or just for the vibrational?
I'd appreciate any comments,
</pre>
</blockquote>
<pre wrap=""><!---->
You should expect to find the difference in the number (and magnitude)
of eigenvalues in (1) and (2).
you should use the eigenvalues obtained from (2) for the
vibrational entropy. There is the mixing between vibrational motions and
rotational motion in (1). This mixing is shown in the last 6 eigenvalues
obtained from (1).
Phuong
_______________________________________________
gmx-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
+++++++++++++++++++++++++++++++++++++++++++
This Mail Was Scanned By Mail-seCure System
at the Tel-Aviv University CC.
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875
------------------------------------------------------
</pre>
</body>
</html>