[gmx-users] mass density

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 2 08:53:25 CET 2005

On Wed, 2005-03-02 at 00:33 -0600, Dinesh Pinisetty wrote:
> Hello everybody,
>         I want to analyze lipid/water/alcohol system.I have following
> questions.
> 1) Does g_density give mass density profiles.
> If we use g_density -f traj.xtc -s topol.tpr -n index.ndx -o density.xvg
> and if we select residue name of alcohol,does this give mass density
> profile of the alcohol.
If all is well it does (or number density)
> 2) How to get the orientation of the water dipole,I mean a graph of mean
> cosine angle of water dipole and bilayer normal.Does any of the commands
> directly give the cosine function values.
try g_h2order

> 3) I have created an index.ndx file such that I had [sn-1] and [sn-2] tails
> in it.I want to look at the order parameter of sn-1 and sn-2.When I used
> g_order its giving me error saying that gr1 atoms does not match with gr1
> atoms.Is there any specific way to prepare an index file for finding order
> parameter using g_order.
don't know.

>  Any suggestions would be greatly appreciated.
> Thanking you,
> Yours sincerely,
> dinesh.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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