[gmx-users] Fwd: Odd behavior in log files for two simulations with only different nstlog for Gromacs 5.0.4
Christopher Neale
chris.neale at alum.utoronto.ca
Sat Feb 14 03:29:19 CET 2015
Not sure about the differences, but focusing on what is similar: you're not getting anything close to the desired temperature (in one case half and in one case 3 times after only 10 integration steps). I suspect that there is something else going wrong. I've never combined the sd integrator with another temperature coupling method, though I have read that the nose-hoover thermostat is more sensitive than other thermostats to unequilibrated initial conditions and tends to oscillate, so I suspect that you're just seeing two different oscillations that have more to do with statistical differences than with the log output frequency.
Try running without nose-hoover and let sd to the temperature coupling for you for a while and then turn on the nose-hoover if you think you need it.
Chris.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Shuxiang Li <xiang693 at gmail.com>
Sent: 13 February 2015 18:08
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Fwd: Odd behavior in log files for two simulations with only different nstlog for Gromacs 5.0.4
Hi Gromacs users,
I’ve recently been running stochastic dynamics simulations
of a coarse-grained DNA system using Gromacs version 5.0.4 (time step =
10fs) and I’ve encountered some odd behavior. I’ve performed two separate
simulations that were set up and run identically, with the exception that
in one simulation I am writing to the log file every simulation step
(nstlog=1) and in the other simulation I’m writing to the log file every 10
simulation steps (nstlog=10). At the start of each simulation (step 0), the
potential energy, kinetic energy, and temperature are identical to each
other. However by the 10th simulation step, the results written to the log
file are very different. For example, for the simulation where nstlog=1 the
kinetic energy is 3.82607e+05 and the temperature is 1.44300e+02 while in
the simulation where nstlog=10, the kinetic energy is 1.67058e+07 and the
temperature is 9.60676e+03. However, the potential energies are identical
for the two simulations, so I think that the trajectories are also probably
identical. In other words, I think the only problem is with the kinetic
energies and temperatures as written to the log file.
I was wondering if anyone in the community could help me explain this
behavior. I'm running Gromacs 5.0.4, but I have seen the same odd behavior
both in Gromacs 5.0 and Gromacs 4.6.5. I’ve included a portion of the log
files and the grompp.mdp from my two simulations below.
Thank you very much for your assistance,
Shuxiang Li
log file 1 (nstlog=1):
###################################
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond Tab. Bonds Angle LJ (SR) Coulomb (SR)
1.12668e+06 -1.10569e+07 9.97976e+04 6.40874e+05 0.00000e+00
Dih. Rest. Potential Kinetic En. Total Energy Temperature
8.54999e+03 -9.18102e+06 7.90352e+05 -8.39067e+06 2.98080e+02
Pressure (bar)
0.00000e+00
......
Step Time Lambda
10 0.10000 0.00000
Energies (kJ/mol)
Bond Tab. Bonds Angle LJ (SR) Coulomb (SR)
1.25536e+06 -1.09081e+07 1.20898e+05 6.47746e+05 0.00000e+00
Dih. Rest. Potential Kinetic En. Total Energy Temperature
1.17815e+05 -8.76625e+06 3.82607e+05 -8.38364e+06 1.44300e+02
Pressure (bar)
0.00000e+00
log file 2 (nstlog=10):
###################################
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond Tab. Bonds Angle LJ (SR) Coulomb (SR)
1.12668e+06 -1.10569e+07 9.97976e+04 6.40874e+05 0.00000e+00
Dih. Rest. Potential Kinetic En. Total Energy Temperature
8.54999e+03 -9.18102e+06 7.90352e+05 -8.39067e+06 2.98080e+02
Pressure (bar)
0.00000e+00
Step Time Lambda
10 0.10000 0.00000
Energies (kJ/mol)
Bond Tab. Bonds Angle LJ (SR) Coulomb (SR)
1.25536e+06 -1.09081e+07 1.20898e+05 6.47746e+05 0.00000e+00
Dih. Rest. Potential Kinetic En. Total Energy Temperature
1.17814e+05 -8.76625e+06 2.54721e+07 1.67058e+07 9.60676e+03
Pressure (bar)
0.00000e+00
grompp.mdp file1 (nstlog=1):
#######################
title = 298 kelvin BD
cpp = /lib/cpp
define =
integrator = sd
comm-mode = Angular
dt = 0.010
nsteps = 1000
nstxout = 100000
nstvout = 100000
nstlog = 1
nstenergy = 100000
nstxtcout = 100000
xtc_grps = system
energygrps = system
nstlist = 25
ns_type = grid
pbc = no
vdwtype = user
coulombtype = user
cutoff_scheme = group
dispcorr = no
tcoupl = nose-hoover
tc_grps = system
tau_t = 10
ref_t = 298
gen_vel = yes
gen_temp = 298
gen_seed = 6789
ld_seed = 6789
bd-fric = 0.0
rlist = 4.0
rcoulomb = 4.0
rvdw = 4.0
grompp.mdp file2 (nstlog=10):
#######################
title = 298 kelvin BD
cpp = /lib/cpp
define =
integrator = sd
comm-mode = Angular
dt = 0.010
nsteps = 1000
nstxout = 100000
nstvout = 100000
nstlog = 10
nstenergy = 100000
nstxtcout = 100000
xtc_grps = system
energygrps = system
nstlist = 25
ns_type = grid
pbc = no
vdwtype = user
coulombtype = user
cutoff_scheme = group
dispcorr = no
tcoupl = nose-hoover
tc_grps = system
tau_t = 10
ref_t = 298
gen_vel = yes
gen_temp = 298
gen_seed = 6789
ld_seed = 6789
bd-fric = 0.0
rlist = 4.0
rcoulomb = 4.0
rvdw = 4.0
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