Hello, I have 125 hexane molecules in a box of 0.25nm3. The desnity I calculate from this number of molecules is approx. 71000 Kg/m3. To make sure that the density remains constant I am doing NPT simulation. From this simulation I see the density is 577 Kg/m3. and the volume is 30 nm3. Please guide me why is this...also how can I get the compressibility for my system?
*Volume 30.9568 0.374111 0.204815 -0.108427 -1.08449 Density (SI) 577.914 6.97804 3.80252 2.02643 20.2684* Thanks, Statistics over 5001 steps [ 0.0000 thru 10.0000 ps ], 21 data sets The term 'Cons. rmsd ()' is averaged over 501 frames All other averages are exact over 5001 steps Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Angle 4390.56 265.163 204.663 58.3917 584.034 Ryckaert-Bell. 986.833 112.503 83.3767 26.1601 261.653 LJ-14 649.581 30.9116 28.8685 3.82766 38.2843 Coulomb-14 -289.755 25.871 9.19928 8.3746 83.7628 LJ (SR) -3367.85 62.5126 55.3718 -10.0486 -100.506 Coulomb (SR) 675.839 21.1543 7.92426 -6.79315 -67.9451 Coul. recip. 927.32 22.6843 7.25885 -7.4434 -74.4489 Potential 3972.53 379.824 316.992 72.469 724.835 Kinetic En. 6331.94 257.353 242.79 29.5579 295.639 Total Energy 10304.5 567.222 484.728 102.027 1020.47 Temperature 297.366 12.086 11.4021 1.38812 13.884 Pressure (bar) -30.0299 746.524 745.665 -12.3992 -124.017 Cons. rmsd () 3.73576e-06 2.80181e-07 2.35022e-07 5.28277e-08 5.28383e-07 Box-X 4.98423 0.0200728 0.0109722 -0.00582152 -0.0582268 Box-Y 2.49212 0.0100364 0.0054861 -0.00291076 -0.0291134 *Volume 30.9568 0.374111 0.204815 -0.108427 -1.08449 Density (SI) 577.914 6.97804 3.80252 2.02643 20.2684* pV -55.9879 1393.39 1391.81 -22.9985 -230.031 #Surf*SurfTen 218.21 4871.45 4871.37 -9.30662 -93.0848 T-HEX 297.366 12.086 11.4021 1.38812 13.884 Lamb-HEX 1.00011 0.000588089 0.000561362 -6.07045e-05 -0.000607166 Heat Capacity Cv: 12.5027 J/mol K (factor = 0.0016519) Isothermal Compressibility: 0.00011012 /bar Adiabatic bulk modulus: 9080.99 bar mdp file: title = Hexane cpp = /lib/cpp ; Run control integrator = md dt = 0.002 ; ps ! nsteps = 5000 ; total 1.0 ps. nstcomm = 1 ; frequency for center of mass motion removal ; Output control nstenergy = 10 ; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps nstxout = 10 ; frequency to write coordinates/velocity/force to output trajectory file nstvout = 0 nstfout = 10 nstlog = 10 ; frequency to write energies to log file nstxtcout = 10 ; Neighbor searching nstlist = 10 ; neighborlist will be updated at least every 10 steps ;ns_type = grid ; Electrostatics/VdW coulombtype = PME vdw-type = cut-off ; Cut-offs rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Temperature coupling Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = HEX ;sol tau_t = 0.1 ;0.1 ref_t = 300 ;300 ; Pressure coupling: Pressure coupling is not on Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Velocity generation Generate velocites is on at 300 K. Manual p155 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ; Bonds constraints = all-bonds constraint-algorithm = lincs pbc=xyz
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