[gmx-users] Problems extending a calculation (in steps and Benchmark)

[Rebeca García Fandiño]

Hello,
I am doing a simulation of a membrane + protein using ffG53a6 in Gromacs.
First I equilibrated at constant volume and then I changed to semi-isotropic pressure.
 
This is my mdp file:
title           = EQUILIBRADO
cpp             = /usr/bin/cpp
include         = -I../top
define          =
constraints     = all-bonds
integrator      = md
dt              = 0.002
nsteps          = 100000
nstxout         = 1000
nstvout         = 1000
nstlog          = 1000
nstenergy       = 1000
nstxtcout       = 1000
nstlist         = 10
ns_type         = grid
rlist           = 1.0
coulombtype     = PME
rcoulomb        = 1.0
vdwtype         = cut-off
rvdw            = 1.4
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
;Berendsen temperature coupling is on
Tcoupl          = berendsen
tau_t           = 0.1     0.1    0.1
tc-grps         = Protein DOPC SOL_NA+_CL-
ref_t           = 310     310    310
; Pressure coupling
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = Semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p                    = 1.0 1.0
compressibility          = 4.6E-5 4.6E-5
ref-p                    = 1.0 1.0
;Generate velocities is on at 310 K
gen_vel         = yes
gen_temp        = 310
gen_seed        = 173529
 
W
hen I did 
 
grompp -f equilibrado3.mdp -c equilibrado2.gro -p ionized_system.top -o equilibrado3.tpr -n index.ndx
mdrun -v -deffnm equilibrado3
 
I got a Benchmark of :
 
               NODE (s)   Real (s)      (%)
       Time:  38960.000  38960.000    100.0
                       10h49:20
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:     93.815     25.746      0.444     54.111
 
(My system is very big, so the Benchmark is reasonable)
 
The next I did was extending the calculation:
 
tpbconv -s equilibrado3.tpr -f equilibrado3.trr -e equilibrado3.edr -n index.ndx -o equilibrado4.tpr -extend 200000
 
Surpringsingly, the calculation reached 504.722 steps (it should have stopped at 300.000 since I had done 100.000 and extended to 200.000 more!) and if I look at the benchmark 
I see:
               NODE (s)   Real (s)      (%)
       Time: 172782.000 172782.000    100.0
                       1d23h59:42
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:     85.694     23.514    100.010      0.240
 
What is obviously incorrect.
 
Anybody knows what could be happening?
 
Thank you very much in advance,
 
Rebeca García Fandiño
Parc Cientific of Barcelona
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