Thanks once again. Ideally I shouldnt do for whole system. Ok.
On Wed, 16 Jul 2008 Justin A.Lemkul wrote : > > >minnale wrote: >> but here I am calculating density for 128 lipids not for 64 lipids. Is it >> right what iam doing? > >The examples on the wiki are just a few illustrative ideas, meant to inspire >the fact that you can analyze whatever subset of your system you wish. You >can certainly analyze all headgroups at once. The point was that, if, for >example, you have a small molecule or protein (or whatever else) interacting >with the surface of one leaflet of the bilayer, you may wish to divide your >structure into different subsets. > >-Justin > >> >>On Wed, 16 Jul 2008 Justin A.Lemkul wrote : >> > >> > >> >minnale wrote: >> >> Thanks for the reply, may be this is trivial question to you >> >>That I know that how to select phosrous atom alone of POPC. >> >>Normally people are using only phosphrous atom or PO4 group ? for density >> calculation ,etc analysis. In one article I found that they have done >> density analysis for PO4 group. >> >>Could you please tell me which one use it for analysis if PO4 how select >> by using make_ndx? >> >>Thanks alot in advance. >> > >> >I have seen both P and PO4 analyzed, as well. It's up to you to decide >> what is most relevant for your situation. >> > >> >I updated the wiki page this morning to include some examples: >> > >> >http://wiki.gromacs.org/index.php/make_ndx >> > >> >-Justin >> > >> >> >> >> >> >>On Wed, 16 Jul 2008 Florian Haberl wrote : >> >> >Hi, >> >> > >> >> >On Wednesday, 16. July 2008, minnale wrote: >> >> > > Hi Users, >> >> > > I want to do analysis of g_density of lipidbilayer so how can I >> select po4 >> >> > > and N(CH3)3 groups seperately by using make_ndx from popc. Can >> anyone tell >> >> > > me detail with which options use? >> >> > > I have checked in archives that create sn1.ndx and sn2.ndx files >> but i >> >> > > didnt get celarly. Thanks in advance >> >> > >> >> >Take first a look on your .gro file and identify the atoms you want to >> select. >> >> > >> >> >try something like: >> >> > >> >> >make_ndx -f your_file.gro >> >> > >> >> >a P* >> >> > >> >> >this should select all atoms with P in your system., it also depends >> on the >> >> >used force field. >> >> > >> >> >Also "h" prints out some inforamation about the selection choices. >> >> > >> >> > >> >> >greetings, >> >> > >> >> >Florian >> >> > >> >> >-- >> >> >> >------------------------------------------------------------------------------- >> >> > Florian Haberl >> >> > Computer-Chemie-Centrum >> >> > Universitaet Erlangen/ Nuernberg >> >> > Naegelsbachstr 25 >> >> > D-91052 Erlangen >> >> > Telephone: +49(0) â 9131 â 85 26573 >> >> > Mailto: florian.haberl AT chemie.uni-erlangen.de >> >> >> >------------------------------------------------------------------------------- >> >> >> >> >> >> >> >>Rediff Shopping >> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL >> PROTECTED]/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null> >> >> >> >> >> >>------------------------------------------------------------------------ >> >> >> >>_______________________________________________ >> >>gmx-users mailing list gmx-users@gromacs.org >> >>http://www.gromacs.org/mailman/listinfo/gmx-users >> >>Please search the archive at http://www.gromacs.org/search before posting! >> >>Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> >-- ======================================== >> > >> >Justin A. Lemkul >> >Graduate Research Assistant >> >Department of Biochemistry >> >Virginia Tech >> >Blacksburg, VA >> >jalemkul[at]vt.edu | (540) 231-9080 >> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> > >> >======================================== >> >> >> >>Rediff Shopping >><http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL >> PROTECTED]/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null> >> > >-- ======================================== > >Justin A. Lemkul >Graduate Research Assistant >Department of Biochemistry >Virginia Tech >Blacksburg, VA >jalemkul[at]vt.edu | (540) 231-9080 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >========================================
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