[gmx-users] surface tension vs. system size
Elisabeth
katesedate at gmail.com
Fri Mar 25 02:46:24 CET 2011
Dear all,
I performed surface tension calculations vs. different system size (NVT, mdp
file is included at the end). The reported surface tension for hydrocarbon I
am studying is 18 mN/m at 20C. I am getting ~ 175 bar nm from g_energy which
means surface tension of around 9 mN/m. For box size 3 3 6 nm I get 202 bar
nm which is 10 mN/m and is closer to the reported one.
0-Are my results reasonable? Is it possible to get closer to the actual
surf. ten? or the current difference can not be improved by molecular
dynamics?
1- I am just wondering how I can decide on the system size given runs
performed (shown below). Which system I can stick to?
2- Can I conclude that surface tension I am getting is equilibrated one?
RMSD is much larger than average!!
There are 125 molecules in a 3 3 3 nm box initially. *F*or 6 6 ? runs: 3 3 3
was replicated in X and Y. (that is 4*125 molecules)
*box size 6 6 18 nm (molecules fill up volume of 6 6 3 and Z direction is
increased to 18 so total size is 6 6 18)
*
Statistics over 898601 steps [ *0.0000 through 1797.2001 ps ]*, 1 data sets
All statistics are over 898601 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 175.32 2.9 1813.06 -17.41
(kJ/mol)
Statistics over 818001 steps [ *0.0000 through 1636.0001 ps* ], 1 data sets
All statistics are over 818001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 175.482 4.9 1814.64 -19.6398
(kJ/mol)
Statistics over 569501 steps [ *500.0000 through 1639.0001 ps* ], 1 data
sets
All statistics are over 569501 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 175.459 5 1815.85 -31.5002
(kJ/mol)
Statistics over 321001 steps [* 1000.0001 through 1642.0001 ps ]*, 1 data
sets
All statistics are over 321001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 168.128 3.9 1812.23 -12.0096
(kJ/mol)
--------------------------------------------------------------------------------------------------------------------------------------------------------------------
*box size 6 6 8 nm. (molecules fill up volume of 6 6 3 and Z direction is
increased to 8 so total size is 6 6 8)
*Statistics over 1000001 steps [* 0.0000 through 2000.0001 ps *], 1 data
sets
All statistics are over 1000001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 177.274 3.9 1819.27 -0.465725
(kJ/mol)*
*
Statistics over 750001 steps *[ 500.0000 through 2000.0001 ps ],* 1 data
sets
All statistics are over 750001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 176.247 3.7 1817.88 12.2119
(kJ/mol)
*
*
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*box size 6 6 6 nm. (molecules fill up volume of 6 6 3 and Z direction is
increased to 6 so total size is 6 6 6)
*Statistics over 532601 steps [ 0.0000 through 1065.2001 ps ], 1 data sets
All statistics are over 532601 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 175.137 2.2 1816.63 -2.51592
(kJ/mol)
Statistics over 282601 steps [ *500.0000 through 1065.2001 ps* ], 1 data
sets
All statistics are over 282601 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 178.413 7.6 1815.25 -21.8612
(kJ/mol)
-------------------------------------------------------------------------------------------------
*box size 3 3 9 nm. (molecules fill up volume of 3 3 3 and Z direction is
increased to 9 so total size is 3 3 9)*
Statistics over 1000001 steps [ 0.0000 through 2000.0001 ps ], 1 data sets
All statistics are over 1000001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 180.985 8.2 3621.55 18.4731
(kJ/mol)
Statistics over 750001 steps [ 500.0000 through 2000.0001 ps ], 1 data sets
All statistics are over 750001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 186.314 4.6 3613.31 -15.9818
(kJ/mol)\
Statistics over 500001 steps [ 1000.0001 through 2000.0001 ps ], 1 data sets
All statistics are over 500001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 181.459 5.5 3614.08 10.9469
(kJ/mol)
-------------------------------------------------------------------------------------------------------------------------------------------------------------
*box size 3 3 6 nm. (molecules fill up volume of 3 3 3 and Z direction is
increased to 6 so total size is 3 3 6)*
Statistics over 1000001 steps [ *0.0000 through 2000.0001 ps* ], 1 data sets
All statistics are over 1000001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 202.46 9.1 3619.78 17.2976
(kJ/mol)
Statistics over 750001 steps [ *500.0000 through 2000.0001 ps* ], 1 data
sets
All statistics are over 750001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
#Surf*SurfTen 201.403 12 3610.81 40.9167
(kJ/mol)
Statistics over 500001 steps [ *1000.0001 through 2000.0001 ps* ], 1 data
sets
All statistics are over 500001 points
Energy Average Err.Est. RMSD Tot-Drift
----------------------------------------------------------------------------
#Surf*SurfTen 212.306 7.7 3607.07 -30.9386
(kJ/mol)
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
3- This last trial gives surf ten of 10 mN/m which is closer tp experimental
18 mN/m, although system is 1/4 smaller in number of molecules than 6 6 ?
runs!
4- Also I am attempting to obtain density profile across the box *6 6
8 nm.*( 6 6 3 is filled up and from Z= 3 to 8 is the empty space). Why
am I
getting Segmentation fault?!
g_density -f *.trr -s *.tpr -o density.xvg
Selected 0: 'System'
trn version: GMX_trn_file (single precision)
Last frame 10000 time 2000.000
Segmentation fault
constraints = all-bonds
constraint-algorithm = lincs
pbc = xyz
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 = 1.2
rcoulomb = 1.2
rvdw = 1.0
fourierspacing = 0.2
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
ewald_geometry = 3dc
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
Thank you !
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