[gmx-users] extending the simulation with modified mdp option
Mark.Abraham at anu.edu.au
Fri Jan 14 00:41:30 CET 2011
On 14/01/2011 10:27 AM, 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.
That should be sufficient. You can also try the wiki's suggestion of
grompp -t old.cpt.
> 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,
> 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
I'd disagree with that last quoted statement, and have updated the wiki
You need to tell us what GROMACS version you're using. There has been at
least one bug fixed in this area in my recent memory, so you may do
better with version 4.5.3.
> 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,
> On Wed, Jan 12, 2011 at 3:06 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at 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
> 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
> 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
> 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.
> Thank you
> 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
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