[gmx-users] extending the simulation with modified mdp option
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 14 00:47:24 CET 2011
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 <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
>
>
> 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
>
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--
========================================
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
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