[gmx-users] micelle center of mass rdf to water

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jan 12 11:11:23 CET 2007

Hi Chris,

Maybe my modified version of trjconv can help. You could use it to 1.
center the system on one atom of a tail of one of your lipids (which
is in the center of your micelle) and 2. distribute all the atoms in
the system such that their distance from that atom is shortest. This
should give you a proper micelle, on which you could perform
subsequent analysis. I'll have to dig a bit to find the right version.
If you're interested or want more information, you can contact me



On 1/12/07, Chris Neale <chris.neale at utoronto.ca> wrote:
> I have a micelle in a box of water. I want to get the radial distance
> profile of different atom types from the center of mass of the micelle.
> This is not as simple as might be imagined because centering the micelle
> does not keep the micelle together, but splits it to the corners of the
> unit cell and the Rg/rdf calculations are incorrect. I found a solution
> as follows:
> trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
> grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
> trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump
> However, now the waters have spread very far away and my
> water-micelleCOM rdf is incorrect. I have tried many things in order to
> fix this:
> trjconv -pbc cluster on the entire trajectory takes way too long
> trjconv -center after trjconv -pbc cluster breaks the micelle apart again.
> anything after the trjconv -pbc nojump stage is futile as the molecules
> continue to exist outside the unit cell
> trjconv -fit translation using the cluster.tpr from above doesn't work
> either.
> I then went on to make a program that will read in my DPC .itp file and
> create a new .itp file that lists all DPCs as one molecule. I did this
> because I remember reading that mdrun does not write broken molecules. I
> therefore used this .itp to create a new .tpr file and gave my original
> .xtc file as input to mdrun -rerun using this new .tpr. I did not get an
> output .xtc file, but I did get a .trr file in which, unfortunately, the
> micelle was split across the unit cell as before.
> Please understand that I have no problem with the simulation going on
> like this, but that (I think) my analysis requires the micelle to be all
> together in the unit cell.
> Any assistance on how to use mdrun -rerun in this way or on any other
> ideas are appreciated. The program to multiply the .itp file is
> available on request. It is 500lines so I didn't include it on this list.
> Chris.
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

More information about the gromacs.org_gmx-users mailing list