Thanks for the reply. As I am new to GROMACS I am not able to understand. I will go through the manual and will get back if I have further questions.<br><br><br><div class="gmail_quote">On Tue, Feb 28, 2012 at 6:00 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im"><br>
<br>
kirtana S wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks for the documentation. Again I have a ligand terminated silica nanoparticle ,what can be the easiest way to approach the topology file for this.<br>
<br>
<br>
</blockquote>
<br></div>
I don't know what the structure is, but I'll assume the .rtp route is probably easier than writing a (presumably) repetitive topology for a relatively large particle. You may or may not need to invoke specbond.dat for cross-links, as pdb2gmx can deal only with linear species via .rtp entries; other bonds are introduced with specbond.dat.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
On Tue, Feb 28, 2012 at 5:46 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
kirtana S wrote:<br>
<br>
For example if I have a polystyrene polymer chains and monomers<br>
of user defined solvent . I need to construct the .itp file by<br>
hand .<br>
<br>
<br>
Polystyrene is most easily generated using .rtp entries in pdb2gmx.<br>
The solvent can be described by manually created .itp files.<br>
<br></div>
<a href="http://www.gromacs.org/__Documentation/How-tos/Polymers" target="_blank">http://www.gromacs.org/__<u></u>Documentation/How-tos/Polymers</a><br>
<<a href="http://www.gromacs.org/Documentation/How-tos/Polymers" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/Polymers</a><u></u>><br>
<br>
<br>
-Justin<br>
<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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