On 8/20/12 1:15 PM, mohammad agha wrote:
Dear Gromacs Users,
I have one problem about the way of computation in the Gromacs with frame and
time. (I work with MARTINI CG)
I have one md.mdp file that the parameters of output control in it is as
follows:
nsteps = 30000000
dt = 0.030
; Output control
nstxout = 2000
nstvout = 2000
nstenergy = 2000
nstlog = 2000
nstxtcout = 2000
xtc_precision = 1000
Consequently, total time of my system is 900000 ps.When I want to obtaine some
information about my system for example RDF by g_rdf command, computation of
Gromacs perfome as follows:
Reading frame 200 time 12000.000
.................300
.................400
.................500
.................600
.................700
...........
...........
...........
Reading frame 2000 time 120000.000
.................3000
.................4000
.................5000
.................6000
.................7000
...........
...........
...........
Last frame 15000 time 900000.000
It means that until frame 2000 reading is 100 to 100 in frames and from 2000 to
end, it is 1000 to 1000.
I don't understand this assertion. You have frames every 60 ps, as expected.
Console output is buffered so that the programs are not wasting time continually
updating the frame number and time value.
Also, I did with this parameters:
; Output control
nstxout = 200
nstvout = 200
nstenergy = 100
nstlog = 200
nstxtcout = 200
xtc_precision = 100
but the result of reading the frames was the same previous.
I want to Gromacs read frames 100 to 100 not 1000 to 1000, because I find
problem when I use -b in g_rdf command. for eaxample, with -b 80000, reading is
only until 860040 ps, Reading frame 13000 time 860040.000 ,not until end of
simulation (900000).
This sounds like the same issue above. The console output may be incomplete.
It's merely a convenience to have an estimate of how long the calculation is taking.
Also, I want to have smaller systems with smaller volume by convert 2000 to
10000 for parameters for output control but I want reading from frame for
computation of properties become 100 frames to 100 frames or 10 frames to 10
frames.
I also don't understand this statement so I can't offer anything to particularly
useful to help.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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