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