[gmx-users] Re: Multiple LINCS Warnings in NVT Equillibration

[ashish24294]

I changed the cut-offs as follows, still isn't helping. I tried restraining
the urea which also didn't work.  I have attached the topology as well. 
topolurea.top
<http://gromacs.5086.x6.nabble.com/file/n5009723/topolurea.top>  

*The nvt.mdp*

title       = UREA_in_WATER NVT equillibration
;define = -DPOSRES_UREA
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 50000     ; 2 * 50000 = 100 ps
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 100       ; save coordinates every 0.2 ps
nstvout     = 100       ; save velocities every 0.2 ps
nstenergy   = 100       ; save energies every 0.2 ps
nstlog      = 100       ; update log file every 0.2 ps
energygrps  = URE
; Bond parameters
continuation    = no            ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints 
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type     = grid      ; search neighboring grid cells
nstlist     = 5         ; 10 fs
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)
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.16      ; grid spacing for FFT
; Temperature coupling
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = URE_Water    ; two coupling groups - more accurate
tau_t       = 0.1   			              ; time constant, in ps
ref_t       = 300                  ; reference temperature, one for each
group, in K
; Pressure coupling
pcoupl      = no        ; no pressure coupling in NVT
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; 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

Using the above nvt.mdp file i got the attached nvt.log   nvt.log
<http://gromacs.5086.x6.nabble.com/file/n5009723/nvt.log>  



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