Dear all,<br><br>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. <br>
<br>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?<br>
<br>1- I am just wondering how I can decide on the system size given runs performed (shown below). Which system I can stick to? <br><br>2- Can I conclude that surface tension I am getting is equilibrated one? RMSD is much larger than average!!<br>
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There are 125 molecules in a 3 3 3 nm box initially. <b>F</b>or 6 6 ? runs: 3 3 3 was replicated in X and Y. (that is 4*125 molecules)<br><br><b>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)<br>
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<br>Statistics over 898601 steps [ <b>0.0000 through 1797.2001 ps ]</b>, 1 data sets<br>All statistics are over 898601 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>
#Surf*SurfTen 175.32 2.9 1813.06 -17.41 (kJ/mol)<br><br><br>Statistics over 818001 steps [ <b>0.0000 through 1636.0001 ps</b> ], 1 data sets<br>All statistics are over 818001 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>#Surf*SurfTen 175.482 4.9 1814.64 -19.6398 (kJ/mol)<br><br>Statistics over 569501 steps [ <b>500.0000 through 1639.0001 ps</b> ], 1 data sets<br>
All statistics are over 569501 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>#Surf*SurfTen 175.459 5 1815.85 -31.5002 (kJ/mol)<br>
<br>Statistics over 321001 steps [<b> 1000.0001 through 1642.0001 ps ]</b>, 1 data sets<br>All statistics are over 321001 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>
#Surf*SurfTen 168.128 3.9 1812.23 -12.0096 (kJ/mol)<br>--------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
<b>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)<br><br></b>Statistics over 1000001 steps [<b> 0.0000 through 2000.0001 ps </b>], 1 data sets<br>All statistics are over 1000001 points<br>
<br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>#Surf*SurfTen 177.274 3.9 1819.27 -0.465725 (kJ/mol)<b><br>
</b><br>Statistics over 750001 steps <b>[ 500.0000 through 2000.0001 ps ],</b> 1 data sets<br>All statistics are over 750001 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>
#Surf*SurfTen 176.247 3.7 1817.88 12.2119 (kJ/mol)<br><b><br></b>-------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
<b>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)<br><br></b>Statistics over 532601 steps [ 0.0000 through 1065.2001 ps ], 1 data sets<br>All statistics are over 532601 points<br>
<br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>#Surf*SurfTen 175.137 2.2 1816.63 -2.51592 (kJ/mol)<br>
<br>Statistics over 282601 steps [ <b>500.0000 through 1065.2001 ps</b> ], 1 data sets<br>All statistics are over 282601 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>
#Surf*SurfTen 178.413 7.6 1815.25 -21.8612 (kJ/mol)<br><br>-------------------------------------------------------------------------------------------------<br><b>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)</b><br>
<br>Statistics over 1000001 steps [ 0.0000 through 2000.0001 ps ], 1 data sets<br>All statistics are over 1000001 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>
#Surf*SurfTen 180.985 8.2 3621.55 18.4731 (kJ/mol)<br><br>Statistics over 750001 steps [ 500.0000 through 2000.0001 ps ], 1 data sets<br>All statistics are over 750001 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>#Surf*SurfTen 186.314 4.6 3613.31 -15.9818 (kJ/mol)\<br><br>Statistics over 500001 steps [ 1000.0001 through 2000.0001 ps ], 1 data sets<br>
All statistics are over 500001 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>#Surf*SurfTen 181.459 5.5 3614.08 10.9469 (kJ/mol)<br>
<br>-------------------------------------------------------------------------------------------------------------------------------------------------------------<br><br><b>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)</b><br>
<br>Statistics over 1000001 steps [ <b>0.0000 through 2000.0001 ps</b> ], 1 data sets<br>All statistics are over 1000001 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>
#Surf*SurfTen 202.46 9.1 3619.78 17.2976 (kJ/mol)<br><br>Statistics over 750001 steps [ <b>500.0000 through 2000.0001 ps</b> ], 1 data sets<br>All statistics are over 750001 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>#Surf*SurfTen 201.403 12 3610.81 40.9167 (kJ/mol)<br><br><br>Statistics over 500001 steps [ <b>1000.0001 through 2000.0001 ps</b> ], 1 data sets<br>
All statistics are over 500001 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>----------------------------------------------------------------------------<br>#Surf*SurfTen 212.306 7.7 3607.07 -30.9386 (kJ/mol)<br>
<br>-------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br><br>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! <br>
<br>4- Also I am attempting to obtain density profile across the box <b>6 6 8 nm.</b> ( 6 6 3 is filled up and from Z= 3 to 8 is the empty space). Why am I getting Segmentation fault?!<br>
<br>g_density -f *.trr -s *.tpr -o density.xvg<br><br>Selected 0: 'System'<br>trn version: GMX_trn_file (single precision)<br>Last frame 10000 time 2000.000 <br>Segmentation fault<br><br><br>
constraints = all-bonds <br>
constraint-algorithm = lincs<br>
pbc = xyz <br> <br>integrator = md <br>dt = 0.002 <br>nsteps = 1000000<br> <br><br>
nstenergy = 100 <br>nstxout = 100 <br> nstlist = 10 <br>ns_type = grid <br><br>coulombtype = PME <br>
vdw-type = Shift <br>rcoulomb-switch = 0 <br>rvdw-switch = 0 <br>rlist = 1.2 <br>rcoulomb = 1.2 <br>
rvdw = 1.0 <br>fourierspacing = 0.2 <br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4 <br>
ewald_rtol = 1e-5<br>optimize_fft = yes<br><br>ewald_geometry = 3dc<br><br>Tcoupl = v-rescale <br>tc-grps = System <br>tau_t = 0.1 <br>
ref_t = 300 <br> <br>gen_vel = yes <br>gen_temp = 300.0 <br>gen_seed = 173529 <br><br><br>Thank you !<br>
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