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p.s. How big is this negative value?<br>
<br>
Ran Friedman wrote:
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Hi,<br>
<br>
Can you post the exact commands you used for EM and NMA?<br>
<br>
Ran<br>
<br>
nahren manuel wrote:
<blockquote cite="mid826474.53862.qm@web45104.mail.sp1.yahoo.com"
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valign="top">Dear Gromacs Users,<br>
<br>
I am trying to calculate Entropy from Normal Mode Analysis.<br>
I minimized the structure to<br>
8.41750710592449e-09<br>
<br>
Then I calculated the normal mode (the mdp file is given below). <br>
<br>
But when i try to calculate the Eigenvalues, I get the following warning<br>
<br>
<br>
One of the lowest 6 eigenvalues has a non-zero value.<br>
This could mean that the reference structure was not<br>
properly energy minimized.<br>
Writing eigenvalues...<br>
<br>
I get only negative eigenvalues.<br>
<br>
Let me also add that I used the same mdp file for minimization changing
the integrator to steep, cg and finally to l-bfgs.<br>
<br>
Best,<br>
nahren<br>
<br>
-----------------------<br>
integrator = nm <br>
constraints = none<br>
define = -DFLEXIBLE<br>
emtol = 0.00000001 <br>
emstep = 0.00000001 <br>
nsteps = 50000 <br>
nstlist = 1 <br>
ns_type = grid <br>
rlist = 1.5 <br>
coulombtype = shift <br>
rcoulomb-switch = 1.0 <br>
rvdw-switch = 1.0 <br>
vdwtype = shift<br>
rcoulomb = 1.3<br>
rvdw = 1.3</td>
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<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: <a class="moz-txt-link-abbreviated"
href="mailto:r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a>
Skype: ran.friedman
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