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hi all,<br>
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.<br>
here are my pr.mdp and md.mdp files,<br>
thanks in advance,<br>
cheers<br>
hayagreevan<br>
<br>
md.mdp:<br>
<br>
define = -DFLEXIBLE<br>
ttle = LD5<br>
cpp = /usr/bin/cpp<br>
constraints = all-bonds<br>
integrator = md<br>
<br>
dt = 0.002<br>
nsteps = 5000<br>
nstcomm = 1<br>
nstxout = 500<br>
nstvout = 0<br>
nstfout = 0<br>
nstlist = 5<br>
ns_type = grid<br>
rlist = 1.0<br>
coulombtype = PME<br>
rcoulomb = 1.0<br>
rvdw = 1.2<br>
fourierspacing ` = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
<br>
; Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>
tau_t = 0.1 0.1 0.1<br>
tc-grps = protein sol NA+<br>
ref_t = 325 325 325<br>
<br>
<br>
;pressure coupling is on<br>
Pcoupl = berendsen<br>
tau_p = 10.0<br>
compressibility = 4.5e-5<br>
ref_p = 3.0<br>
<br>
;generate velocities is on at 300K.<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
<br>
pr.mdp<br>
<br>
title = vii<br>
cpp = /usr/bin/cpp<br>
define = -DPOSRES<br>
constraints = all-bonds<br>
integrator = md<br>
dt = 0.002 ; ps !<br>
nsteps = 5000 ; total 10 ps.<br>
nstcomm = 1<br>
nstxout = 250<br>
nstvout = 1000<br>
nstfout = 0<br>
nstlog = 10<br>
nstenergy = 10<br>
nstlist = 5<br>
ns_type = grid<br>
rlist = 1.0<br>
rcoulomb = 1.2<br>
rvdw = 1.2<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
<br>
; Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>
tc-grps = Protein SOL NA+<br>
tau_t = 0.1 0.1 0.1<br>
ref_t = 300 300 300<br>
; Energy monitoring<br>
; Pressure coupling is not on<br>
Pcoupl = berendsen<br>
tau_p = 15.0<br>
ref_p = 10.0<br>
compressibility = 4.5e-5<br>
; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
<br>
<br>
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