Rebeca García Fandiño wrote:
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
What is the time given on the initial frame (from the logfile?) What does
gmxcheck tell you about your .trr and .edr files (are they the times you think
they are?). If you're seeing a time indicator of 504.722, that would be the
time (in ps), not the step number, so it's almost as if your new run started
over from 0 and ran for a short time.
What happens if you use grompp to extend your run, instead of tpbconv? It might
be interesting to see if there's a difference. Also, you could try tpbconv
-time 100000 -until 300000, also to see if it would make a difference. This
will test to see if your tpbconv executable is functioning correctly or not.
-Justin
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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