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On 9/05/2011 10:43 PM, toby10222224 wrote:<br>
<br>
Please use a useful subject line when replying to a digest.<br>
<br>
<blockquote cite="mid:201105092043104521991@sina.com" type="cite">
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<div><font color="#000080" face="Verdana" size="2">I mean all the
positions of the carbon atoms are invariant during mdrun. In
the .gro file, carbonyl carbon and oxygen atoms are defined as
group 'Carbonyl' and the rest every single carbon atom is
defined as 'CNT'.</font></div>
</blockquote>
<br>
A .gro file doesn't have groups.<br>
<br>
<blockquote cite="mid:201105092043104521991@sina.com" type="cite">
<div><font color="#000080" face="Verdana" size="2"> For the use of
'freeze groups', the group 'CNT' should be freezed. But for
group 'Carbonyl', as oxygen atom is allowed to move, it is not
appropriate to freeze group 'Carbonyl'. </font></div>
</blockquote>
<br>
Sure, I think you want a freeze group of all the nanotube carbons,
and all the carbonyl oxygens. make_ndx will allow you make such a
union.<br>
<br>
<blockquote cite="mid:201105092043104521991@sina.com" type="cite">
<div><font color="#000080" face="Verdana" size="2">I wonder
whether the same atom can be included in two or more groups.
If it can be, I can ignore the group name defined in the .gro
file and redefine groups by using command 'make_ndx'. Then I
am able to <font color="#000000">make use of index </font></font></div>
</blockquote>
<br>
Groups aren't defined in the coordinate file. If you use a GROMACS
utility that can accept an index file as input, and do not provide
one, then GROMACS generates some standard ones from the coordinate
file. In the case of make_ndx, these are then written out when you
quit.<br>
<br>
<blockquote cite="mid:201105092043104521991@sina.com" type="cite">
<div><font color="#000080" face="Verdana" size="2"><font
color="#000000">groups to define an appropriate freezegrp
in </font>the .mdp file. All the carbon atoms of the CNT
(inclduing carbonyl carbon atoms) are supposed to be defined
as 'CNT', and carbonyl carbon atoms and oxygen oxygens are
'Carbonyl'. Group 'CNT' is the freeze group. Is it feasible
for this idea?</font></div>
</blockquote>
<br>
You're in charge... I don't know what external entity is dictating
what you are "supposed" to do :-)<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:201105092043104521991@sina.com" type="cite">
<div><font color="#000080" face="Verdana" size="2">Thank you!</font></div>
<div> </div>
<div><font color="#c0c0c0" face="Verdana" size="2">2011-05-09 </font></div>
<font color="#000080" face="Verdana" size="2">
<hr style="width: 100px;" align="left" color="#b5c4df" size="1">
</font>
<div><font color="#c0c0c0" face="Verdana" size="2"><span>toby10222224</span>
</font></div>
<hr color="#b5c4df" size="1">
<div><font face="Verdana" size="2">
</font><font face="Verdana" size="2">Message: 4</font></div>
<div>
<div><font face="Verdana" size="2">Date: Mon, 09 May 2011 06:58:04 -0400</font></div>
<div><font face="Verdana" size="2">From: "Justin A. Lemkul" <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a></font></div>
<div><font face="Verdana" size="2">Subject: Re: [gmx-users] freeze the carbonyl carbon atoms</font></div>
<div><font face="Verdana" size="2">To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a></font></div>
<div><font face="Verdana" size="2">Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:4DC7C8BC.5090907@vt.edu"><4DC7C8BC.5090907@vt.edu></a></font></div>
<div><font face="Verdana" size="2">Content-Type: text/plain; charset=ISO-8859-1; format=flowed</font></div>
<div><font face="Verdana" size="2">toby10222224 wrote:</font></div>
<div><font face="Verdana" size="2">> Hi:</font></div>
<div><font face="Verdana" size="2">> </font></div>
<div><font face="Verdana" size="2">> I have a carbon nanotube (CNT) and several carbonly groups (C=O). </font></div>
<div><font face="Verdana" size="2">> Meanwhile the carbonly carbon atoms are part of the CNT. That is to say </font></div>
<div><font face="Verdana" size="2">> an oxygen atom is attached to one carbon atom of the CNT to form a </font></div>
<div><font face="Verdana" size="2">> carbonyl group. All the carbon atoms are supposed to be fixed, while </font></div>
<div><font face="Verdana" size="2">> carbonyl carbon and oxygen atoms are supposed to have bond interactions. </font></div>
<div><font face="Verdana" size="2">> I can freeze the rest carbon atoms of the CNT, but how to deal with the </font></div>
<div><font face="Verdana" size="2">> carbonly atoms?</font></div>
<div><font face="Verdana" size="2">> </font></div>
<div><font face="Verdana" size="2">By "fixed," do you mean their positions should be invariant (i.e. freeze groups) </font></div>
<div><font face="Verdana" size="2">or that their bond lengths should be constrained? If the former, then you </font></div>
<div><font face="Verdana" size="2">should be able to make use of index groups to define an appropriate freezegrp in </font></div>
<div><font face="Verdana" size="2">the .mdp file. If the latter, use "constraints = none" in the .mdp file, and </font></div>
<div><font face="Verdana" size="2">write a [constraints] directive for the bonds you do wish to be constrained.</font></div>
<div><font face="Verdana" size="2">-Justin</font></div>
<div><font face="Verdana" size="2">> Any suggestions are appreciated!</font></div>
<div><font face="Verdana" size="2">> Thank you in advance!</font></div>
<div><font face="Verdana" size="2">> </font></div>
<div><font face="Verdana" size="2">> 2011-05-09</font></div>
<div><font face="Verdana" size="2">> ------------------------------------------------------------------------</font></div>
<div><font face="Verdana" size="2">> toby10222224</font></div>
<div><font face="Verdana" size="2">> </font></div>
<div><font face="Verdana" size="2">-- </font></div>
<div><font face="Verdana" size="2">========================================</font></div>
<div><font face="Verdana" size="2">Justin A. Lemkul</font></div>
<div><font face="Verdana" size="2">Ph.D. Candidate</font></div>
<div><font face="Verdana" size="2">ICTAS Doctoral Scholar</font></div>
<div><font face="Verdana" size="2">MILES-IGERT Trainee</font></div>
<div><font face="Verdana" size="2">Department of Biochemistry</font></div>
<div><font face="Verdana" size="2">Virginia Tech</font></div>
<div><font face="Verdana" size="2">Blacksburg, VA</font></div>
<div><font face="Verdana" size="2">jalemkul[at]vt.edu | (540) 231-9080</font></div>
<div><font face="Verdana" size="2"><a class="moz-txt-link-freetext" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></font></div>
<div><font face="Verdana" size="2">========================================</font></div>
</div>
</blockquote>
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