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

Sat Dec 3 06:49:51 CET 2011

On 3/12/2011 4:42 PM, pragna lakshmi wrote:
> 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
>

The atom that has the greatest force after EM is the same one for which 
LINCS warnings arise later. That's worth paying attention to. Read the 
advice about diagnosing unstable systems on the link Justin gave you 
last time.

>
> # 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

http://www.gromacs.org/Documentation/Terminology/Thermostats

> ; 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

It's probably not useful to re-generate velocities after the 
position-restrained step.

Mark

>
> # 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 
> <mailto: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
>
>     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 <http://vt.edu> | (540) 231-9080
>     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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