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>.' My 'mdp' options are: title = production-dynamics ;warnings = 10 cpp = /lib/cpp ;DEFINE = -DPOSRES DEFINE = -DFLEXIBLE 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 Please help. thank you, Rama On Wed, Jan 12, 2011 at 3:06 PM, Justin A. Lemkul <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 | (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 >
-- 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