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.abra...@anu.edu.au <mailto:mark.abra...@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
    <jalem...@vt.edu <mailto:jalem...@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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--
T.Pragna Lakshmi,
Junior Scientist,
Vision Research Center,
Sankara Netralaya,
Chennai,
India.
Pin: 600006.




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