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On 4/22/2011 6:48 PM, Mark Abraham wrote:
<blockquote cite="mid:4DB140D6.5080104@anu.edu.au" type="cite">
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On 4/22/2011 4:54 PM, majid hasan wrote:
<blockquote cite="mid:28714.94092.qm@web38301.mail.mud.yahoo.com"
type="cite">
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<div style="color: rgb(0, 0, 0);">Dear All,</div>
<div style="color: rgb(0, 0, 0);"><br>
</div>
<div style="color: rgb(0, 0, 0);">I am doing a MD simulation
of dna, and cnt in water. I get a stable simulation in which
DNA, and CNT wiggles around there positions, but they don't
seem to be attracted towards each other. CNT starts in the
middle of the box and just moves a little, and DNA starts at
top right corner of the box and remains there throughout the
simulation.</div>
<div style="color: rgb(0, 0, 0);"><br>
</div>
<div style="color: rgb(0, 0, 0);">movie of .trr file is here:</div>
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<div><font class="Apple-style-span" face="'times new roman',
'new york', times, serif"><span><a moz-do-not-send="true"
target="_blank"
href="http://phas.ubc.ca/%7Emajid/Project/cntdna.mpg">http://phas.ubc.ca/~majid/Project/cntdna.mpg</a></span></font></div>
<div><font class="Apple-style-span" face="'times new roman',
'new york', times, serif"><br>
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<div style="color: rgb(0, 0, 0);">My .mdp files are placed
here (both .mdp files are same except for the value of
integrator):</div>
<div style="color: rgb(0, 0, 0);"><a moz-do-not-send="true"
href="http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp">http://phas.ubc.ca/~majid/Project/lbfgs.mdp</a> (used
for EM)</div>
<div style="color: rgb(0, 0, 0);"><a moz-do-not-send="true"
href="http://phas.ubc.ca/%7Emajid/Project/md.mdp">http://phas.ubc.ca/~majid/Project/md.mdp</a>
(used for MD)</div>
<div style="color: rgb(0, 0, 0);"><br>
</div>
<div style="color: rgb(0, 0, 0);"><br>
</div>
<div style="color: rgb(0, 0, 0);"><br>
</div>
<div style="color: rgb(0, 0, 0);">I created cnt, and dna using
following commands:</div>
<div style="color: rgb(0, 0, 0);">For dna: pdb2gmx -f dna.pdb
-o dna.gro -p dna.top -ff select (Selected amber99sb, and
TIP3P water model)</div>
<div style="color: rgb(0, 0, 0);">For cnt: g_x2top -f cnt.gro
-o cnt.top -ff select -pbc (selected amber99sb)</div>
<div style="color: rgb(0, 0, 0);">For mixing and solvation:
genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 -try
20 </div>
<div style="color: rgb(0, 0, 0);">genbox -cp cntdna.gro -cs
spc.gro -o cntdnasol.gro </div>
<div style="color: rgb(0, 0, 0);"><br>
</div>
<div style="color: rgb(0, 0, 0);">In the dna.top file,
amber99sb/ions.itp, and a position restraint file was also
included along with tip3p.itp. I mentioned it because I am
not sure why would it add ions and position restraints on
adding water? <br>
</div>
</div>
</blockquote>
<br>
#including molecule .itp files adds nothing to the system - only
the potential to have molecule type(s). The system is defined in
the [system] directive, and must match the corresponding
coordinate file.<br>
<br>
<blockquote cite="mid:28714.94092.qm@web38301.mail.mud.yahoo.com"
type="cite">
<div style="font-family: 'times new roman','new
york',times,serif; font-size: 12pt; color: rgb(0, 0, 0);">
<div style="color: rgb(0, 0, 0);">It seems that something is
wrong with non-bonded interactions, but I don't understand
what?</div>
</div>
</blockquote>
<br>
Why aren't you following a proper equilibration protocol before
trying to make observations? You might be using position
restraints, have your species too far apart, or simply have not
simulated long enough to observe any movement. 200ps is an
eye-blink.<br>
</blockquote>
<br>
Actually, you simulated 20ps. Your MD timestep is 0.2fs, which is
unreasonably short. 100,000 of them is far too short to see anything
happen.<br>
<br>
Mark<br>
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