[gmx-users] Check for bad contacts and/or reduce the timestep

Sat Dec 3 06:42:18 CET 2011

Thank u for reply. I did energy minimization and equilibration step. It
converged in 696 steps which is shown below.

Step=  692, Dmax= 9.2e-03 nm, Epot= -7.12587e+05 Fmax= 7.62150e+03, atom=
2099
Step=  693, Dmax= 1.1e-02 nm, Epot= -7.12588e+05 Fmax= 9.72038e+03, atom=
2099
Step=  695, Dmax= 6.6e-03 nm, Epot= -7.12670e+05 Fmax= 9.39830e+02, atom=
2099

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 696 steps
Potential Energy  = -7.1266969e+05
Maximum force     =  9.3982965e+02 on atom 2099
Norm of force     =  2.1967674e+01

# md.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 1000000 ; total 50 ps.
nstcomm = 1
nstxout = 500 ; output coordinates every 1.0 ps
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1 0.1 0.1
tc-grps = protein ZN IMP sol NA+
ref_t = 300 300 300 300 300
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
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

# pr.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 50000 ; total 20.0 ps.
nstcomm = 1
nstxout = 250 ; output coordinates every 0.5 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = V-rescale
tau_t = 0.1 0.1 0.1 0.1 0.1
tc_grps = protein ZN sol IMP NA+
ref_t = 300 300 300 300 300
; Pressure coupling is on
Pcoupl = no
pcoupltype = isotropic
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

#em.mdp file

title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 2000
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME ; Use particle-mesh ewald
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01

I need further help to trouble shoot this problem.

On Sat, Dec 3, 2011 at 10:46 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> pragna lakshmi wrote:
>
>> Hi,
>>     I am trying to run protein-ligand complex simulation. At the final MD
>> run step it is showing the following error. Can anybody tell me the
>> solution for this error?
>>
>>
> http://www.gromacs.org/**Documentation/Errors#LINCS.**
> 2fSETTLE.2fSHAKE_warnings<http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings>
>
> There are hundreds of threads in the archive with the same issue and
> several possible solutions.  Please consult the link above (and referenced
> pages), as well as other posts.
>
> If you need further help diagnosing the problem, please post a complete
> .mdp file, as well as a description of prior minimization and equilibration.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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-- 
T.Pragna Lakshmi,
Junior Scientist,
Vision Research Center,
Sankara Netralaya,
Chennai,
India.
Pin: 600006.
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