GROMACS version: 2020.2
Hi, I am trying to use GROMACS to analyze the deuterium order parameter of POPC in a NAMD trajectory. I kept getting the error message “There are inconsistent shifts over periodic boundaries in a molecule type consisting of 59504 atoms. The longest distance involved in such interactions
is 6.236 nm which is above half the box length. Either you have excessively
large distances between atoms in bonded interactions or your system is
exploding.”
I’m trying to figure out what went wrong in my process and would appreciate some help with this.
Here is my process:
- created a tpr file with pdb, top files and a dummy mdp file (the top file was created from the pdb file with the vmd topo pluggin):
gmx grompp -p system.top -c system.pdb -f system.mdp -maxwarn 10 -o system.tpr - created an index file for POPC sn-1:
selected carbons on POPC sn-1:
r POPC & a C22
…
r POPC & a C218
deleted irrelevant groups:
del 0-29 - convert dcd to trr with VMD
- converted trr to xtc and tried to fix pbc error:
gmx trjconv -f traj.trr -s system.pdb -pbc whole -o traj.xtc
gmx trjconv -f traj.xtc-s -pbc nojump -o traj2.xtc
gmx trjconv -f traj2.xtc -ur compact -o traj3.xtc
gmx trjconv -f traj3.xtc -center -o traj4.xtc
(I tried these steps in different orders and also tried to adjust the box size with ‘-box x, x,x’ but nothing seemed to work) - gmx order -f traj4.xtc -s system.tpr -n sn1.ndx -od SCD_POPC_sn1.xvg
Thanks so much!