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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