Nimesh Jain wrote:
I am attaching the file, The simulation doesn't seem to crash, the log
gets updated for sure. Hope you can make some sense of it.
A few things:
1. Please do not attach entire log files. That took forever for my mail client
to download with no ability to abort.
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
2. Since I had already downloaded such an enormous file, I looked through it
anyway, and found several potential problems:
a. You probably have problems in your tables:
"WARNING: For the 4981 non-zero entries for table 2 in table_SA_SB.xvg the
forces deviate on average 44% from minus the numerical derivative of the potential"
b. Your value of nstlog is nonsense: "nstlog = 1215752192" indicates that mdrun
did not find a reasonable value, i.e. you have exceeded the maximum size for an
integer. Use a large, but sensible, setting.
c. Your system is exploding, with a temperature of 1.14469e+04.
I suspect that the large log file is produced by the instability of the system,
and hence you're getting a huge amount of diagnostic information, much of which
is somewhat cryptic.
-Justin
On Thu, Dec 16, 2010 at 1:50 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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>
<mailto: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> <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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Nimesh Jain
Graduate Student
Biomedical Engineering
Northwestern University
--
========================================
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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