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