Hi Mark, Justin, Thanks for your help. The details are helpful to improve my MD simulation. Also i need update my gromacs version from 4.5.1 to 4.5.3.
Thanks again, Rama On Thu, Jan 13, 2011 at 3:47 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Ramachandran G wrote: > >> thanks for your reply. >> Still i have the same problem. >> My aim is to extend my simulation from 6ns to 7ns. >> >> First i prepared the tpr as >> >> grompp_mpi -f nve.mdp -c nve6-g.tpr -o nve7-g.tpr -n crom.ndx >> >> where 'nve6-g.tpr' is my old 'tpr' . In the 'nve.mdp' file i have changed >> the option of storing the 'nstxout' from 1 to 100. >> That is the only change i have done. >> >> For simulation i do, >> >> mpirun -nolocal -np 8 -machinefile machine mdrun_mpi -nice 0 -v -s >> nve7-g.tpr -o nve-g.trr -c nve-g.gro -e nve-g.edr -cpi nve6-g.cpt -g >> md-g.log -append -cpo nve7-g.cpt -pd >> >> From the gromacs website, >> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations >> i understood that i need to use the option of 'tpbconv' also to extend the >> simulation. It says that >> 'If your |old.cpt| is for a run that has finished, then use |tpbconv >> -extend |after grompp <http://www.gromacs.org/grompp> and before mdrun < >> http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun>.' >> >> >> > The easiest thing for you to do is to simply extend your run with tpbconv > and ignore grompp. If you just need to reduce output volume, post-process > the trajectory with trjconv. Otherwise, you have 6 ns of coordinates at > every step, then 1 ns of coordinates every 100 steps. The frame interval > mismatch will likely cause numerous Gromacs tools to fail, anyway. > > > My 'mdp' options are: >> >> title = production-dynamics >> ;warnings = 10 >> cpp = /lib/cpp >> ;DEFINE = -DPOSRES >> DEFINE = -DFLEXIBLE >> > > Flexible water should not be used for MD. > > http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html > > > constraints = none >> ;constraint_algorithm = shake >> integrator = md >> dt = 0.0005 ; >> nsteps = 2000000 ; >> ;nstcomm = 1 ; reset c.o.m motion >> nstlist = 10 >> ns_type = grid >> nstenergy = 1 ; print energies >> nstlog = 1 ; print to logfile >> nstvout = 0 ; write velocities >> nstxout = 100 ; collect data in fs (write coords) >> ;nstxtcout = 0 ; to print corrdinates to xtc trajectory >> energygrps = Protein CROM HOH1 HOH2 SOL >> nstfout = 0 >> coulombtype = shift >> fourierspacing = 0.12 >> pme_order = 4 >> vdwtype = switch >> rvdw = 1.0 >> rvdw_switch = 0.9 >> rlist = 1.2 >> rcoulomb = 1.0 >> rcoulomb-switch = 0.9 >> pbc = xyz >> ;dispcorr = Ener >> continuation = yes >> ;Berendsen temperature coupling is on >> Tcoupl = no ; temperature bath (yes, no) >> ;tau_t = 0.1 >> ;tc-grps = system >> ;ref_t = 300 >> ;Berendsen Pressure coupling is on >> pcoupl = no ; pressure bath (yes, no) >> ;pcoupltype = isotropic >> ;tau_p = 0.5 >> ;compressibility = 4.5e-05 >> ;ref_p = 1.0 >> ;Generate velocities is on at 300 >> gen_vel = no ; generate initial velocities >> ;gen_temp = 300.0 ; initial temperature >> ;gen_seed = 173529 ; random seeD >> >> > You haven't set the tinit parameter in this file. In conjunction with the > fact that this .mdp file is for 1 ns, it will start at time zero and run to > 1 ns. If you're trying to pick up from the end of a 6-ns simulation, you > have two options: > > 1. Set tinit=6000 and leave nsteps and dt alone. Pass the .cpt file to the > -t flag of grompp and run it as if it were a new simulation, then > concatenate the output. > > 2. Set tinit=0 and set nsteps=350000 to generate a complete 7-ns .tpr file. > Pass this to mdrun in conjunction with your .cpt file from the end of your > 6-ns run. > > 3. Use tpbconv and ignore grompp entirely, then post-process appropriately. > > > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4 > > -Justin > > >> Please help. >> thank you, >> Rama >> >> >> >> On Wed, Jan 12, 2011 at 3:06 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Ramachandran G wrote: >> >> Hi gmx-users, >> I tried extending one of simulation with modified mdp option. >> First i used the command, >> >> grompp -f new.mdp -c old.tpr -o new.tpr >> >> then i used the command to extend >> >> tpbconv -s new.tpr -extend timetoextendby -o next.tpr >> >> >> Then, >> >> mdrun -s next.tpr -cpi previous.cpt >> >> >> I surprised to see the following simulation output, >> WARNING: This run will generate roughly 2059394074917430016 Mb >> of data >> >> starting mdrun 'GROningen MAchine for Chemical Simulation in water' >> >> 2000000 steps, infinite ps (continuing from step 12000000, >> 6000.0 ps). >> step 12000000 performance: 0.3 ns/day step 12000100 >> performance: 0.8 ns/day step 12000200 performance: 0.8 ns/day >> step 12000300 performance: 0.8 ns/day step 12000400 >> performance: 0.8 ns/day step 12000500 >> performance: 0.8 ns/day step 12000600 performance: 0.8 ns/day >> step 12000700 performance: 0.8 ns/day step 12000800 >> performance: 0.8 ns/day step 12000900 performance: 0.8 >> ns/day step 12001000 >> performance: 0.8 ns/day step 12001100 performance: 0.8 ns/day >> -------------------------------------------------- >> Is this correct? Why it needs to generate that much huge Mb of >> data? >> >> I have extended for 1000.0ps but it shows 'infinite ps'. >> can anybody help me if there is error made in my procedure? >> >> >> It seems like you're trying to extend your run using both grompp and >> tpbconv, which is not correct. Use one or the other. >> >> If you want a real answer to this question, please post real >> commands, not just the generic format of what should be correct. >> Also possibly useful is the contents of the .mdp file you used. >> >> -Justin >> >> Thank you >> Rama >> >> >> >> >> -- ======================================== >> >> 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@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> >> > -- > ======================================== > > 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 >
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