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

Chris Neale chris.neale at utoronto.ca
Fri Jan 12 01:14:34 CET 2007

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 

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.


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