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Hello!
I am trying to conduct energy scoring using the gRINN software. I have successfully downloaded it and have attempted to input my gmx simulation files but have run into some issues. gRINN requires the TPR, TOP, and XTC files of the simulation. I originally ran it using the original files which included the solvent and ions in addition to the proteins, but that was taking very long. I then read that gRINN recommends removing the solvents and ions from the files and leaving just the proteins. I followed instructions they gave to remove the ions and solvent from the TOP and TPR file, although they didn’t give instructions to remove the ions and solvent from the XTC file. I used instructions on page 25 of this manual to remove the solvents and ions from the TOP and TPR files: https://grinn.readthedocs.io/_/downloads/en/latest/pdf/
Below is the md.mdp file I created with the instructions; I simply removed the temperature coupling portion as it said. Perhaps there are other sections which I must have removed?
title = Protein-ligand complex MD simulation
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 5000000 ; 2 * 5000000 = 10000 ps (10 ns)
dt = 0.002 ; 2 fs
; Output control
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save coordinates every 10.0 ps
; Bond parameters
continuation = yes ; continuing from NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds to H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighbor searching and vdW
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; largely irrelevant with Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Pressure coupling
pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction is not used for proteins with the C36 additive FF
DispCorr = no
; Velocity generation
gen_vel = no ; continuing from NPT equilibration
I first tried running gRINN using the new TPR and TOP files without the solvent or ions and the same XTC file. However, I received this error saying that the trajectory file could not be read:
I would greatly appreciate any guidance with these errors! Thank you in advance!
