[gmx-users] extending the simulation with modified mdp option

[Ramachandran G]

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 <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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