Hi Rama, It sounds to me that the best prog. to use will be "g_density". This useful programme calculates partial densities of system components. You can then deduce the position of a small molecule inside a lipid bilayer by computing partial densities of the lipids, small molecule and solvent (spc?) in your system.
You will prob. need to use "make_ndx" to setup specific index groups. use the "-h" flag for further details re. the prog. or any other gmx prog. Use the -sl option to slice the box up into the desired no. of slices, the default is 10. This will increase your statistics and result in smoother gaussians. The default for this prog. is Z (or the bilayer normal for the "bilayer people" amongst us :) ) so you don't need to change the default! hope that helps. Kia > Message: 2 > Date: Tue, 21 Mar 2006 10:12:05 -0800 (PST) > From: Rama Gullapalli <[EMAIL PROTECTED]> > Subject: [gmx-users] Position of a molecule in a bilayer > To: gmx-users@gromacs.org > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Dear GMX ers > I would like to compute the position of a small molecule inside a lipid bilayer as a function of its position along the Z axis. Which GMX program is best suited for this? > > I tried using g_traj, but I got some weird results when i computed the COM position of a DPPC molecule. The COM position of DPPC was crossing the center of the lipid bilayer which is weird. > Thanks > Rama > > > -- Kia Balali-Mood PhD, CBiol, MIBiol Postdoctoral Research Associate, Department of Biochemistry, Oxford University, OX1 3QU, UK sansom.biop.ox.ac.uk/kia/ , tel. +44 (0)1865 275 (380 or 275) _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
