GROMACS version: 2018.4 and 2022.3
GROMACS modification: No
Hi! new user here.
I have tried to use 2018.4 and 2022.3 for running NVT on my system and it sucessfully finishes the simulation and outputs my .xtc, .edr and my .log file but not my .trr file. However, my energy minimization does output a .trr file. I have a metal oxide surface and a protein, so I tested the same nvt on just the metal oxide surface and the same problem occured where no .trr file was produced. I’m not sure what is wrong with my mdp or the way I’m calling mdrun. In any case, no errors occured in my error_prod.txt.
Here I will attach my minimization mdp called em.mdp, my nvt_short.mdp, and md_nvt.log.
md_nvt.log (42.3 KB)
em.mdp (4.4 KB)
NVT 100 ps equilibration
; RUN CONTROL PARAMETERS
integrator = md ; Leap-frog algorithm
dt = 0.001 ; 1 fs timestep
nsteps = 10000 ; Number of steps (100 ps)
comm-mode = Linear ; Remove center of mass translational velocity
nstcomm = 100 ; Frequency (steps) for center of mass motion removal
comm-grps = System ; Group(s) for center of mass motion removal
; OUTPUT CONTROL OPTIONS
nstcalcenergy = 100 ; Calculate energies each 100th step
nstenergy = 5000 ; Save energies every 5 ps
nstlog = 5000 ; Update log file every 5 ps
nstxout-compressed = 5000 ; Write xtc trajectory every 5 ps
energygrps = System ; Which energy group(s) to write to disk
compressed-x-grps = System ; Group(s) to write to xtc file
; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme = Verlet ; Generate a pair list with buffering (GPU support)
nstlist = 100 ; Frequency to update the neighbor list and long range forces
ns-type = grid ; Method to determine neighbor list (simple, grid)
pbc = xyz ; Periodic Boundary Conditions
rlist = 1.4 ; Cut-off for making neighbor list (short range forces)
periodic-molecules = yes ; Periodic molecules in the simulation box
verlet-buffer-tolerance = 0.005 ; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = pme ; Particle Mesh Ewals
coulomb-modifier = Potential-shift-Verlet ; Potential shift with Verlet cut-off scheme
rcoulomb-switch = 0 ; Where to start switching [nm]
rcoulomb = 1.4 ; Real space cut-off
vdw-type = cut-off ; Simple cut-off
vdw-modifier = Potential-shift-Verlet ; Potential shift with Verlet cut-off scheme
rvdw-switch = 0 ; Where to start switching [nm]
rvdw = 1.4 ; Real space cut-off
DispCorr = EnerPres ; Dispersion corrections to both the potential and pressure
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12 ; PME grid
; EWALD/PME/PPPM parameters
pme-order = 4 ; Cubic interpolation
ewald-rtol = 1e-05 ; The relative strength of the Ewald-shifted direct potential at rcoulomb
ewald-rtol-lj = 0.001 ; The relative strength of the dispersion potential at rvdw
lj-pme-comb-rule = Geometric ; The combination rules used to combine VdW-parameters in the reciprocal space of LJ-PME
ewald-geometry = 3d ; The Ewald sum is performed in all three dimensions
; OPTIONS FOR WEAK COUPLING ALGORITHMS
tcoupl = v-rescale ; Bussi thermostat
tc-grps = H306 Protein Water_and_ions ; Groups to couple to separate temperature baths
tau-t = 1.0 1.0 1.0 ; Time constant for temperature coupling
ref-t = 303 303 303 ; Desired temperature (K)
Pcoupl = no ;berendsen ; No p coupling
Pcoupltype = anisotropic ; Anisotropic barostat
nstpcouple = -1 ; Coupling frequency is set to nstlist
ref-p = 1.0 1.0 1.0 0.0 0.0 0.0 ; Desired pressure (bar)
tau-p = 5.0 ; Time constant for pressure coupling
compressibility = 5e-7 5e-7 5e-5 0.0 0.0 0.0 ; TiO2 TiO2 H2O compressibility
; VELOCITY GENERATION
gen-vel = yes ; Generate velocities according to Maxwell distribution
gen-temp = 303 ; Temperature for Maxwell distribution
; CONSTRAINTS
constraints = h-bonds ; Constrain h-bonds
I think I need my .trr file in order to run PLUMED in gui.