Nimesh Jain wrote:
Well, no. I got a 20GB log file when nstlog was 1000. When I changed it
to 10000, the log file was about 1 MB after a few minutes of simulation
which means that it will be in GBs in a few days.
Then look at what it's writing. Is it giving the output you expect? Are all
replicas written to the same log file? I haven't used REMD since Gromacs 3.x,
when replicas were written to separate logs, I don't know if it's changed. I'd
be far more concerned with outputting full precision coordinates and velocities
every 10 ps - that will likely occupy huge amounts of disk space.
And as an aside, when you directly say a certain .mdp file produces a 20 GB log
file, the users of this list will expect that to be accurate. If you're not
telling the whole truth, then it makes it hard to diagnose any issues and
discourages people from helping you. Accurate reporting makes for faster
resolution.
-Justin
On Wed, Aug 11, 2010 at 10:49 AM, Gaurav Goel <gauravgoel...@gmail.com
<mailto:gauravgoel...@gmail.com>> wrote:
You've set the frequency of writing to log file as
'nstlog = 100000'.
Given that 'nsteps = 100000000', you're writing to
the log file only 1000 times. Do you get a 20GB md.log file with
these settings?
-Gaurav
On Wed, Aug 11, 2010 at 10:52 AM, Nimesh Jain
<nimeshjain2...@u.northwestern.edu
<mailto:nimeshjain2...@u.northwestern.edu>> wrote:
Hi,
I am having some problem in my simulations related to log files.
The file sizes are enormous, its like after 3 days of simulation
I had a 20 GB md.log file. One of my grompps looks like this:
[tau_t is very low because I am using bd and it doesn't work
otherwise]. [I am doing a replica exchange with 10,000 as
exchange frequency]
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
nstlog = 100000
nstenergy = 1000
nstxtcout = 1000
xtc-precision = 1000
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 P260 SA SB
energygrp_table = A A A T A G A C A P260 A SA A
SB T T T G T C T P260 T S
A T SB G G G C G P260 G SA G SB C C C P260 C SA C SB
P260 P260 P260 SA P260 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 = 0.0001
ref_t = 260.00
Pcoupl = No
andersen_seed = 815131
gen_vel = yes
gen_temp = 260.0000
gen_seed = 1993
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions
are excluded
energygrp_excl =
Please let me know if anyone knows whats the problem.
Thanks,
Nimesh
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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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