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<DIV><FONT color=#000080 size=2 face=Verdana>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'. 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>
<DIV><FONT color=#000080 size=2 face=Verdana>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 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>
<DIV><FONT color=#000080 size=2 face=Verdana>Thank you!</FONT></DIV>
<DIV><FONT color=#000080 size=2 face=Verdana></FONT> </DIV>
<DIV><FONT color=#c0c0c0 size=2 face=Verdana>2011-05-09 </FONT></DIV><FONT
color=#000080 size=2 face=Verdana>
<HR style="WIDTH: 100px" align=left color=#b5c4df SIZE=1>
</FONT>
<DIV><FONT color=#c0c0c0 size=2 face=Verdana><SPAN>toby10222224</SPAN>
</FONT></DIV>
<HR color=#b5c4df SIZE=1>
<DIV><FONT size=2 face=Verdana>
<DIV></DIV>Message: 4</DIV>
<DIV>
<DIV>Date: Mon, 09 May 2011 06:58:04 -0400</DIV>
<DIV>From: "Justin A. Lemkul" <jalemkul@vt.edu></DIV>
<DIV>Subject: Re: [gmx-users] freeze the carbonyl carbon atoms</DIV>
<DIV>To: Discussion list for GROMACS users <gmx-users@gromacs.org></DIV>
<DIV>Message-ID: <4DC7C8BC.5090907@vt.edu></DIV>
<DIV>Content-Type: text/plain; charset=ISO-8859-1; format=flowed</DIV>
<DIV></DIV>
<DIV></DIV>
<DIV></DIV>
<DIV>toby10222224 wrote:</DIV>
<DIV>> Hi:</DIV>
<DIV>> </DIV>
<DIV>> I have a carbon nanotube (CNT) and several carbonly groups (C=O). </DIV>
<DIV>> Meanwhile the carbonly carbon atoms are part of the CNT. That is to say </DIV>
<DIV>> an oxygen atom is attached to one carbon atom of the CNT to form a </DIV>
<DIV>> carbonyl group. All the carbon atoms are supposed to be fixed, while </DIV>
<DIV>> carbonyl carbon and oxygen atoms are supposed to have bond interactions. </DIV>
<DIV>> I can freeze the rest carbon atoms of the CNT, but how to deal with the </DIV>
<DIV>> carbonly atoms?</DIV>
<DIV>> </DIV>
<DIV></DIV>
<DIV>By "fixed," do you mean their positions should be invariant (i.e. freeze groups) </DIV>
<DIV>or that their bond lengths should be constrained? If the former, then you </DIV>
<DIV>should be able to make use of index groups to define an appropriate freezegrp in </DIV>
<DIV>the .mdp file. If the latter, use "constraints = none" in the .mdp file, and </DIV>
<DIV>write a [constraints] directive for the bonds you do wish to be constrained.</DIV>
<DIV></DIV>
<DIV>-Justin</DIV>
<DIV></DIV>
<DIV>> Any suggestions are appreciated!</DIV>
<DIV>> Thank you in advance!</DIV>
<DIV>> </DIV>
<DIV>> 2011-05-09</DIV>
<DIV>> ------------------------------------------------------------------------</DIV>
<DIV>> toby10222224</DIV>
<DIV>> </DIV>
<DIV></DIV>
<DIV>-- </DIV>
<DIV>========================================</DIV>
<DIV></DIV>
<DIV>Justin A. Lemkul</DIV>
<DIV>Ph.D. Candidate</DIV>
<DIV>ICTAS Doctoral Scholar</DIV>
<DIV>MILES-IGERT Trainee</DIV>
<DIV>Department of Biochemistry</DIV>
<DIV>Virginia Tech</DIV>
<DIV>Blacksburg, VA</DIV>
<DIV>jalemkul[at]vt.edu | (540) 231-9080</DIV>
<DIV>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</DIV>
<DIV></DIV>
<DIV>========================================</DIV>
<DIV></DIV>
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