my gromacs is giving me this LINC ERROR.i found in the mailing list about this and found two suggestion, one to define it as dflexible and another to increase the tau_p to 20(my initial was 0.5).I did increase it step by step in some 20 runs, still the problem persists.the LINC error is right from 0th step.Can any one help me out on this.
here are my pr.mdp and md.mdp files,
thanks in advance,
cheers
hayagreevan
md.mdp:
define = -DFLEXIBLE
ttle = LD5
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.002
nsteps = 5000
nstcomm = 1
nstxout = 500
nstvout = 0
nstfout = 0
nstlist = 5
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.2
fourierspacing ` = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1
tc-grps = protein sol NA+
ref_t = 325 325 325
;pressure coupling is on
Pcoupl = berendsen
tau_p = 10.0
compressibility = 4.5e-5
ref_p = 3.0
;generate velocities is on at 300K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
pr.mdp
title = vii
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 10 ps.
nstcomm = 1
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 5
ns_type = grid
rlist = 1.0
rcoulomb = 1.2
rvdw = 1.2
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein SOL NA+
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Energy monitoring
; Pressure coupling is not on
Pcoupl = berendsen
tau_p = 15.0
ref_p = 10.0
compressibility = 4.5e-5
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
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