[gmx-users] make_ndx problem

[minnale]

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) − 9131 − 85 26573
>>  >>  >  Mailto: florian.haberl AT chemie.uni-erlangen.de
>>  >>   >-------------------------------------------------------------------------------
>>  >>
>>  >>
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>>  >-- ========================================
>>  >
>>  >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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>>
>
>-- ========================================
>
>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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