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.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> 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@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-requ...@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@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-requ...@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.
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