GROMACS version: 2022.5-plumed_2.9.0
GROMACS modification: Yes/No
Hello developers,
I am using REST2 method in gromacs 2022.5 patched with plumed-2.9.0.
I am simulating IDP with 57 residues. When i strip water from trajectory using -pbc flag with command
gmx trjconv -f production.xtc -n index.ndx -o trajout.xtc -pbc whole -center -s production.tpr
It shows me following error:
Program: gmx trjconv, version 2022.5-plumed_2.9.0
Source file: src/gromacs/pbcutil/mshift.cpp (line 823)
Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 790 atoms. The longest distance involved in such interactions is
9.511 nm which is above half the box length. This molecule type consists of
muliple parts, e.g. monomers, that are connected by interactions that are not
chemical bonds, e.g. restraints. Such systems can not be treated. The only
solution is increasing the box size.
The simulatin box were set up with 3 nm distance between protein atoms and edge of the box. I am not understanding what is longest distance interactions involved? As i use the cutoff 0.9 nm for long range interaction. Please guide me .
Thanks,
Munazzah Fatima Ansari