[gmx-users] Check for bad contacts and/or reduce the timestep
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Dec 3 07:32:04 CET 2011
On 3/12/2011 5:15 PM, pragna lakshmi wrote:
> 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.
Such a conclusion would be premature, given your inappropriate use of
thermostats and the information in the URL Justin provided...
Mark
>
> On Sat, Dec 3, 2011 at 11:19 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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 <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
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto: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
>> <mailto: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
> <mailto: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
> <mailto: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/20111203/47c04448/attachment.html>
More information about the gromacs.org_gmx-users
mailing list