Hello,
Background
I am needing to rerun a trajectory to compute the center of mass(COM) for two groups in a molecule.
I am trying to output the COM to the out put file.
However the output has an accompanying line with the warning “inconsistent image flags” with every output
I want to address this warning as I need my COM to be correct in the rerun as well as produce an output file without the warning in order to use the file in program in which it requires COM to be right after one another
ie
COM 1 COM 2
12 3 4 12 3 7
12 4 3 12 3 5
…….
without the warning wedged in-between.
Question
Anyways my question lies in some ideas of how can I debug this error/warning.
Right now input file reads in a restart file using “read_restart”
I define all my potentials and groups and then get to where I believe my source of error and confusion lie
compute A_CoM antrecene com
compute P_CoM pyrene com
thermo_style custom c_A_CoM[1] c_A_CoM[2] c_A_CoM[3] c_P_CoM[1] c_P_CoM[2] c_P_CoM[3] # variables written to the output
thermo ${out} # how often writes to output
dump 3 linker custom ${dumptrj} npt_NR_folding.lammpstrj id type xs ys zs # writes trajectory in normal format
rerun npt_NR_eps17_300ns_link.lammpstrj first 1000 every 1000 dump x y z box yes scaled no format native
I believe what is happening is that the input file is reading from the restart file to set up the simulation box then gets to rerun in which reads the trajectory file like read_dump and the uses the trajectories to map output in which is inconsistent with the initial
coordinates given from the read_restart file. If this is the point can someone direct me towards a solution to write a better input file for a rerun?
If the warning is unrelated and I need to search elsewhere for a answer let me know as well
Much Appreciated
Michael Goytia
Graduate Student
University of Utah Chemistry Department