Hi,
For one thing; to keep density constant (as in fixed) you want NVT, not
NPT. NPT could, depending on your starting state, allow for initial
drift in the system size.
Cheers,
Erik Marklund
Moeed skrev:
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
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[email protected] http://folding.bmc.uu.se/
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
