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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); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;">Dear All,</div>
<div style="color: rgb(0, 0, 0); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: rgb(0, 0, 0); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;">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); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: rgb(0, 0, 0); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;">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',
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<div style="color: rgb(0, 0, 0); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;">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); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;"><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); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;"><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); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: rgb(0, 0, 0); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: rgb(0, 0, 0); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: rgb(0, 0, 0); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;">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); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;">For cnt:
g_x2top -f cnt.gro -o cnt.top -ff select -pbc (selected
amber99sb)</div>
<div style="color: rgb(0, 0, 0); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;">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); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;">genbox -cp
cntdna.gro -cs spc.gro -o cntdnasol.gro </div>
<div style="color: rgb(0, 0, 0); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;"><br>
</div>
<div style="color: rgb(0, 0, 0); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;">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); font-family: 'times new
roman','new york',times,serif; font-size: 12pt;">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>
<br>
Mark<br>
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