Justin,<br>Thank you for your response. My simulation will involve around 30 chains of polymer along with varying amounts of different salts. For instance LiPF6, LiClO4 and larger molecules like [1,3-dimethylimidazolium]PF6 and I am looking for the best way to incorporate these. I guess I am a little stumped as to the best method for generating these. Should I make separate .gro and topology files for these? <br>
Regards,<br>Caleb<br>PS. I haven't researched this part as much so it is possible this has already been answered and I just haven't come across this. <br><br><br><div class="gmail_quote">On Sun, May 23, 2010 at 10:47 AM, 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Caleb Tormey wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello all,<br>
I have just started working with GROMACS and simulation in general. I will be doing simulation of PEO with various ions and need a little help. I have read a great deal of the documentation and now edited the appropriate .rtp and.itp files to generate my polymer from a .pdb file using pdb2gmx and it seems to be generating my topology and .gro files correctly. <br>
My question is if I wish to keep a static bond length do I address this in the bond information or is there something in the .mdp file that will address this? <br>
</blockquote>
<br></div>
Use the "constraints" keyword in your .mdp file. See the manual.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I also would like some suggestions for a few other things. To make my preliminary polymer I used a molecular modeling/editor program called Avogadro but was wondering if there is something better to use to create the random walk long chain polymer? <br>
</blockquote>
<br></div>
There are several programs that can build molecules, like xLeap (part of AmberTools) and even VMD has some capabilities for building molecules. I don't know about polymers specifically.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Also, I was just going to create my own ion files and use genion to incorporate those into the simulation but didn't know if this was the best way to do this.<br>
<br>
</blockquote>
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To what files are you referring? Are you introducing new parameters of some sort? Be aware that pre-defined ion parameters are included as part of all the force field parameter sets packaged with Gromacs, so any new parameters must be validated before being used.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
And lastly when I need to create a multiple polymer simulation my plan was to use genconf and generate a crystal with the appropriate number of polymers and then just heat it up to melt it. This seems to be a good way to do it however, another person in my group who used NAMD used a program called PackMol and had some success and was wondering if anyone else had used this program and would recommend this route?<br>
<br>
</blockquote>
<br></div>
Either way should work fine. PackMol does a good job of generating initial configurations given geometrical constraints, but your procedure should work if you do sufficient heating to change the initial structure.<br><font color="#888888">
<br>
-Justin</font><div class="im"><br>
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Thank you in advanced.<br>
Regards,<br>
Caleb<br>
<br>
</blockquote>
<br></div><div><div></div><div class="h5">
-- <br>
========================================<br>
<br>
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>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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