4.0.7
Statistics over 733801 steps [ 0.0000 thru 1467.6001 ps ], 1 data sets
All averages are exact over 733801 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 203.778 3623.99 3623.98
-0.00203751 -2.99026
Statistics over 483401 steps [ 500.0000 thru 1466.8000 ps ], 1 data sets
All averages are exact over 483401 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 203.129 3612.58 3612.28
0.168686 163.086
-----------------------------------------------------------------------------------------------------------------
4.5.3
Statistics over 732501 steps [ 1.0000 through 1466.0000 ps ], 1 data sets
All statistics are over 73251 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 2374.49 570 21081.3 -3251.38
(bar nm)
Statistics over 384501 steps [ 1000.0000 through 1769.0000 ps ], 1
data sets
All statistics are over 38451 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 2610.25 1000 21109.9 4638.38
(bar nm)
Statistics over 483001 steps [ 500.0000 through 1466.0000 ps ], 1 data
sets
All statistics are over 48301 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 1645.07 390 20288.3 -174.289
(bar nm)
On 22 March 2011 23:56, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 23/03/11, *Elisabeth * <katesed...@gmail.com
<mailto:katesed...@gmail.com>> wrote:
On 22 March 2011 22:46, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Elisabeth wrote:
On 22 March 2011 22:31, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>> wrote:
Elisabeth wrote:
Hello,
I did two simulations on the same system using
versions 4.0.7
and 4.5.3. It seems like the unit of surface
tension is not the
same in these versions because I am getting ~250
KJ/mol an in
4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can
be converted
into bar nm? Can anyone help please.
Is this from g_energy output? In past versions,
everything was
printed as "kJ/mol," even quantities that obviously
weren't, like
temperature, pressure, etc.
Yes, so why are the results so different. I am using
exactly the same mdp file.!
Any pressure-related quantity is going to be subject to
enormous fluctuations. This has been discussed within the
last few days. Without seeing the .mdp file and a
description of the system, it's hard for anyone to comment on
what the results might mean.
Thanks. I am working on a pure alkane system, in a box of 3X3X3
which is extended in Z to create liq/air interface. That is 3X3X6
. What could be reason for such a big difference in results from
two version? Thanks alot!
Look at the size of the fluctuations printed by g_energy. If
they're comparable or larger than your differences, then you are
not observing a statistically significant difference. Over just
2ns of a small system, that's likely to be the case. Damping such
fluctuations requires large simulations or long times or both.
You are also generating velocities at the start of this run, so
probably you are including spurious measurements on
non-equilibrated configurations in your statistics. If you'd
thought to tell us your command lines, I wouldn't be guessing :-)
You can fix this with g_energy -b, but really you should separate
your equilibration from your production run, even if you don't
really need to, so that all your workflows have similar
properties. Then when you come back to repeat some analysis in a
month's time, you don't have to remember to ignore the first 1ns
of this simulation...
Mark
integrator = md
dt = 0.002
nsteps = 1000000
nstenergy = 100
nstxout = 100
nstlist = 10
ns_type = grid
coulombtype = PME
vdw-type = Shift
rcoulomb-switch = 0
rvdw-switch = 0
rlist = 1.1
rcoulomb = 1.1
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
;optimize_fft = yes
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
pbc = xyz
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
constraints = all-bonds
constraint-algorithm = lincs
-Justin
--
========================================
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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