<html><body><div style="color:#000; background-color:#fff; font-family:verdana, helvetica, sans-serif;font-size:12pt"><div><span>Thanks for your reply.</span></div><div><span>Best Regards</span></div><div><br></div> <div style="font-family: verdana, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Wednesday, November 30, 2011 11:27 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] g_select<br> </font> <br>
<br><br>mohammad agha wrote:<br>> Thanks for your reply, but how can I define residue numbers of one micelle from between 10 micelle that all of them are same and only were differ at the number of monomer in micelle.<br>> May I know how, please?<br><br>Well, now the problem is potentially more complicated. Two approaches:<br><br>1. Using make_ndx, you can create an index file of any micelle if you know all of the residue numbers. Please type "help" at the make_ndx prompt for example usage. It is easy to do.<br><br>2. If you do not know which residues comprise the micelle(s) and you don't want to figure it out manually (I wouldn't), then you need g_select with some geometric criteria. Again, there is help available (see g_select -h for how to invoke help) and search the archives for related posts.<br><br>It would be far more efficient for you and for those who might help you if you post what you've tried and failed at, rather
than leaving us to guess what might work.<br><br>-Justin<br><br>> <br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* mohammad agha <<a ymailto="mailto:mra_bu@yahoo.com" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>>; Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Wednesday, November 30, 2011 7:03 PM<br>> *Subject:* Re: [gmx-users] g_select<br>> <br>> <br>> <br>> mohammad agha wrote:<br>> > Dear Prof.<br>> ><br>> > I have a system consists of 10 micelle after production simulation. How can I select a micelle with 92 monomer?<br>> > I know that I should use from g_select, but I don't know which
argument is proper for me. I also checked -select help in g_select program.<br>> > Please help me.<br>> ><br>> <br>> If you just need an index group with a single micelle, use make_ndx and choose the residue numbers that comprise the micelle. g_select can do the same, but this tool is better suited for more complex operations and creation of dynamic indices.<br>> <br>> -Justin<br>> <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]vt.edu | (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>> ========================================<br>> <br>> <br><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]vt.edu | (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>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www
interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> <br>> <br><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]vt.edu | (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>========================================<br>-- gmx-users mailing
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