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I need to run md simulation on my protein with an unnatural residue (formyl glycine). so I had to download charmm27.ff from SwissSidechain - A database of non-natural sidechains server to create the required topology. Then used 2 versions of GROMACS. the first one is gromacs-2016.4 applied to make topology, solavation and energy minimization . the second one is applied to run NVT/NPT and MD on GPU. but when issued this command
gmx mdrun -deffnm md_0_1 -nb gpu
to run NVT on GPU , faced this error:
can not run short-ranged nonbonded interactions on a GPU because there is no detected.
the NVT.mdp file which I used is:
title = CHARMM27 ARSA NVT equilibration
define = -DUSE_OLD_C36m
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 200000 ; 2 * 200000 = 400 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw-switch = 1.0
; 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 ; modified Berendsen thermostat
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 off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = no ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
I would be really grateful if anyone can help me to understand and solve it out.
sincerly
Farial
informative file