[gmx-users] Protein moves out of box after several simulations, how to fix it?

Marc Hömberger hoembi at gmail.com
Wed May 23 17:30:42 CEST 2012


I have several (12) simulations running in which I simulate a protein
in a water box (cubic 9x9x9). For all simulations I can  see the
After a few simulations (total time of 7.6ns) the protein moves out of
the water box - for all the twelve simulations. Since the following
simulation is started with the output .gro file of the prior
simulation the protein moves further and further out of the box.  I
have no idea if this is a problem because of periodic boundaries or if
this is a problem with my vmd installation. Can anyone give me a hint
what I could to to fix this and not have to restart all the runs?

I am using a script I used before and I am doing everything like last
time but last time I did not see this behavior of the protein. I am
using vmd to look at the protein and its trajectory (commands see

FYI the commands I use to setup the simulations (just an example of two):
grompp -f md2.mdp -c Protein-struct_md1.gro -p Protein.top -o Protein_md2.tpr
mdrun -nt 3 -s Protein_md2.tpr -o Protein_md2.trr -x Protein_md2.xtc
-c Protein-struct_md2.gro -g Protein_md2.log
grompp -f md3.mdp -c Protein-struct_md2.gro -p Protein.top -o Protein_md3.tpr
mdrun -nt 3 -s Protein_md3.tpr -o Protein_md3.trr -x Protein_md3.xtc
-c Protein-struct_md3.gro -g Protein_md3.log
and so on and so forth.

GROMACS version is 4.5.5
VMD version is 1.9.1.

Thanks in advance
Marc Hoemberger

More information about the gromacs.org_gmx-users mailing list