GROMACS version: 2022.02
GROMACS modification: No
When I run eneconv program with -dt parameter equal to same dt of 4.0 ps used for trajectory out in simulation I don’t get any warnings as in:
gmx eneconv -f Solv${state}.edr -o last_half.edr -b 5000 -e 10000 -dt 4
but if I want save every other energy frame run such as this:
gmx eneconv -f Solv${state}.edr -o last_half.edr -b 5000 -e 10000 -dt 8
I get these WARNINGS but I can still run gmx energy, however I don’t know if I can trust it.
WARNING: missing energy sums at time 9928.000000
WARNING: missing energy sums at time 9936.000000
This was original MDP file.
title = Protein-ligand complex NPT equilibration
;define = -DPOSRES ; position restrain the protein and ligand
; Run parameters
integrator = sd ; leap-frog integrator
nsteps = 2500000 ; 0.004 * 2500000 = 5000 ps = 5 ns
dt = 0.004 ; 2 fs
; Output control
nstenergy = 1000 ; save energies every 4.0 ps, = 1000 * 0.004 ps
nstlog = 1000 ; update log file every 4.0 ps, = 1000 * 0.004 ps
nstxout-compressed = 1000 ; save coordinates every 4.0 ps, = 1000 * 0.004 ps