[gmx-users] RE: log files
Nimesh Jain
nimeshjain2010 at u.northwestern.edu
Wed Aug 11 16:52:08 CEST 2010
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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