GROMACS version: 2022,1
GROMACS modification: No
I’m trying to run my MD on our GPU node and I’m facine a problem with
-update gpu: I have the following issue :
Inconsistency in user input: Update task on the GPU was required, but the following condition(s) were not satisfied: The number of coupled constraints is higher than supported in the GPU LINCS code.
I saw it is link to the LINCS parameters, so I put “constraints=none” to try but it doesn’t work either.
So my question is : What are the correct parameters to fully the the MD on GPU :) ?
Here’s my MDP parameters if you need :
integrator = md ; leap-frog algorithm nsteps = 500000 ; 0.002 * 500000.0 = 1000.0 ps or 1.0 ns dt = 0.002 ; 2 fs ; Output control nstxout = 10000 ; save coordinates every 10 ps nstvout = 10000 ; save velocities every 10 ps nstxtcout = 10000 ; xtc compressed trajectory output every 10 ps nstenergy = 10000 ; save energies every 10 ps nstlog = 10000 ; update log file every 10 ps nstcomm = 1000 ; center of mass motion removal ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; (even heavy atom-bH bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 25 ; with Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) rlistlong = 1.0 ; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; v-rescale is used now to have a canonical space tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group,in K ; Pressure coupling is on 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 DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off gen_temp = 300 ; reference temperature, for protein in K