[gmx-users] simulation crashed because of LINCS error

[sonali dhindwal]

Hello All,

With regard to my previous post 
http://www.mail-archive.com/gmx-users@gromacs.org/msg30557.html
I have done postion restrained energy minimisation  using  POSRES.itp file obtained from pdb2gmx. so that there should not be any large change in the strucutre of the protein.
And after that I did equilbration using following mdp file

title               = protein
cpp                 = /usr/bin/cpp
define              = -DPOSRES
constraints         = all-bonds
integrator          = md
dt                  = 0.002 ; ps !
nsteps              = 10000 ; total 20.0 ps.
nstcomm             = 1
nstxout             = 250     ; collect data every 0.5 ps
nstvout             = 1000
nstfout             = 0
nstlog              = 10
nstenergy           = 10
nstlist             = 5
ns_type             = grid
rlist               = 0.9
coulombtype         = PME
rcoulomb            = 0.9
rvdw                = 1.4
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              = V-rescale
tc-grps             = Protein Non-Protein
tau_t               = 0.1     0.1 
ref_t               = 300     300  
; Pressure coupling is on
Pcoupl              = berendsen
tau_p               = 0.5
compressibility     = 4.5e-5
ref_p               = 1.0
; Generate velocites is on at 300 K.
gen_vel             = yes
gen_temp            = 300.0
gen_seed            = 173529

After this, I put the molecule for simulation using the following .mdp file

title               = protein
cpp                 = /usr/bin/cpp
constraints         = all-bonds
integrator          = md
dt                  = 0.002 ; ps !
nsteps              = 500000 ; total 1000 ps, 1 ns.
nstcomm             = 1
nstxout             = 500     ; collect data every 1 ps
nstvout             = 0
nstfout             = 0
nstlist             = 5
ns_type             = grid
rlist               = 0.9
coulombtype         = PME
rcoulomb            = 0.9
rvdw                = 1.4
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              = V-rescale
tc-grps             = Protein Non-Protein
tau_t               = 0.1     0.1 
ref_t               = 300     30
; Pressure coupling is on
Pcoupl              = berendsen
tau_p               = 0.5
compressibility     = 4.5e-5
ref_p               = 1.0
; Generate velocites is on at 300 K.
gen_vel             = yes
gen_temp            = 300.0
gen_seed            = 173529

but simulation has crashed showing the error too many Too many LINCS warnings (1000)
I checked previous posts, it is given that it may be due to incomplete equilibration or putting so many constraints.
So can you please help me in correcting it.
Thanks and regards.

--
Sonali Dhindwal

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