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,
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>.'
I'd disagree with that last quoted statement, and have updated the wiki
accordingly.
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.
Mark
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
<mailto: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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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