Nimesh Jain wrote:
I set nstlog = 100000000000, and still I get a 5MB log file within a
minute of starting the sim. It seems absurd, but its happening :(
Well, a log file will always be written with header information, etc, although 5
MB does seem quite large. The better question is whether or not it continues to
get updated, causing the file size to increase. If it is, investigate what the
contents are. Is the simulation crashing, causing thousands of lines of LINCS
warnings to be printed? Is it normal output, but at a different frequency than
what was specified?
-Justin
On Thu, Dec 16, 2010 at 10:05 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Nimesh Jain wrote:
Hi,
I am trying to simulate a system of 880 particles with implicit
solvent using brownian dynamics, but the simulation generates
huge log files (it writes md.log files at a rate of almost
5MB/minute) and this crashed my system since I ran out of space :(
My mdp file looks like this:
include =
define =
integrator = bd
tinit = 0
dt = 0.001
nsteps = 100000000 ;100000
simulation_part = 1
init_step = 0
comm-mode = Angular
nstcomm = 1
comm-grps =
emtol = 0.01
emstep = 1.5
nstxout = 10000
nstvout = 10000
nstfout = 10000
nstenergy = 1000
nstxtcout = 1000
xtc-precision = 1000
nstlog = 0
xtc-grps =
energygrps =
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 8.95
coulombtype = user
rcoulomb-switch = 0
rcoulomb = 8.95
epsilon-r = 1
vdw-type = user ;cutoff
rvdw-switch = 0
rvdw = 8.95
DispCorr = No
table-extension = 1
; Seperate tables between energy group pairs
energygrps = A T G C P300 SA SB
energygrp_table = A A A T A G A C A P300 A SA A
SB T T T G T C T P300 T SA T SB G G G C G P300 G SA G
SB C C C P300 C SA C SB P300 P300 P
300 SA P300 SB SA SA SA SB SB SB
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.10
Tcoupl = Nose-Hoover
tc-grps = System
tau_t = 0.001
This doesn't seem like a reasonable setting for tau_t; grompp should
have warned you about that since dt = tau_t!
ref_t = 300.00
Pcoupl = No
andersen_seed = 815131
gen_vel = yes
gen_temp = 300.0000
gen_seed = 1993
Please let me know if there is a solution to write smaller mdp
files. I have set nstlog = 0 , but even that doesn't work!
Set nstlog to some incredibly large number, then, and it will only
output a few times. It seems strange that nstlog = 0 didn't
suppress the .log file output as it would any of the other nst*
settings.
-Justin
Thanks
Nimesh
--
========================================
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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--
========================================
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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