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

Sat Dec 3 07:15:51 CET 2011

I understood that the system has large velocities. Since simulation has
been stopped at Step 226040, time 452.08 (ps) can i conclude that error is
because of any invalid parameters in topology file generated by server for
ligand.

On Sat, Dec 3, 2011 at 11:19 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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> 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 | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
>  --
> T.Pragna Lakshmi,
> Junior Scientist,
> Vision Research Center,
> Sankara Netralaya,
> Chennai,
> India.
> Pin: 600006.
>
>
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

-- 
T.Pragna Lakshmi,
Junior Scientist,
Vision Research Center,
Sankara Netralaya,
Chennai,
India.
Pin: 600006.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111203/107fb322/attachment.html>