GROMACS version: 2018
GROMACS modification: No
Dear all,
I’m trying to perform a simple MD run of a box a POPC membrane with water and some ions. I obtained the gro, itp, and mdp files from Jambäck and Lyubartsev’s Website (http://www.fos.su.se/~sasha/SLipids/).
Unfortunately, I’m having an issue already in gmx grompp showing the following error:
ERROR 1 [file md_mem.mdp, line 54]:
Right hand side ‘10.0 10.0’ for parameter ‘tau-p’ in parameter file is not
a real value
I fixed already some incompatibilities of the mdp file with Gromacs 2018 (it seems to be an older mdp file), but can’t find what wrong here.
Below my mdp file. Happy to hear any other feedback, since I haven’t optimized the entire mdp file yet and it’s my first time doing lipid membrane simulations.
Thanks a lot!
Jacek
md.mdp:
integrator = md ; MD integrator
tinit = 0
dt = 0.002 ; 2 fs timestep
nsteps = 500000 ; Number of steps
pbc = xyz ; Periodic boundary conditions in xyz
comm-mode = linear
nstcomm = 1
comm-grps = SOL upper lower ; Remove COM for monolayers separately
; OUTPUT CONTROL OPTIONS
nstxout = 0 ; Do not want .trr-files
nstxout-compressed = 100 ; But do want .xtc-files
nstvout = 0 ; No velocities in output
nstfout = 0 ; No forces in output
nstenergy = 100 ; .edr-file output
energygrps = POPC Water_and_ions ; Energy groups
; OPTIONS FOR ELECTROSTATICS AND VDW
cutoff-scheme = Verlet
nstlist = 10 ; Update neighbor list between cut-offs
ns_type = grid ; Fastest option
coulombtype = pme ; Particle mesh Ewald, do not change
pme_order = 4 ; cubic interpolation
rcoulomb = 1.4 ; Real-space cut-off
; This is different from the paper but
; since PME is used this will only speed
; things up!
rlist = 1.0 ; Short-range neighbor list
vdwtype = cut-off
rvdw = 1.4 ; Slightly different from the original papers but we used this in our recent work,
; DOI: 10.1039/C3CP44472D. Unofficial tests have shown that the bilayers still
; behaves properly when using as short values as 1.0, but please verify this
; before using such a short cut-off. rlistlong can then be removed.
DispCorr = EnerPres ; Dispersion corrections to both the potential and pressure
table-extension = 1
fourierspacing = 0.12 ; PME grid
; OPTIONS FOR WEAK COUPLING ALGORITHMS
tcoupl = V-rescale ; Thermostat, v-rescale is also fine
tc-grps = POPC Water_and_ions ; Couple lipids and SOL seperatly
tau-t = 0.5 0.5 ; Time constant for temperature coupling
ref-t = 300 300 ; Desired temperature (K)
Pcoupl = parrinello-rahman ; Barostat
Pcoupltype = semiisotropic ; Pressure in xy and z couple separately
ref-p = 1.013 1.013 ; Desired pressure (bar)
tau-p = 10.0 10.0 ; Time constant for pressure coupling
compressibility = 4.5e-5 ; Same as for water
; CONSTRAINTS
constraints = all-bonds ; Constrain all bonds
constraint-algorithm = Lincs ; With Lincs
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy