[gmx-users] extending the simulation with modified mdp option
Ramachandran G
gtrama at gmail.com
Fri Jan 14 02:10:48 CET 2011
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 <jalemkul at 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 <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
>
> ========================================
> --
> gmx-users mailing list gmx-users at 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!
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