On 2011-12-27 17:57, Theodora García wrote:
Dear all
I am starting some MD simulations aimed to calculate the volume of a
solute in water as a function of the concentration. First I ran a
simulation of a box with 4124 SPC water molecules (similar number of
molecules that will be later used with my solute) for which I got the
following results after ~7.5 ns:
dispcorr = enerpres
Statistics over 3762001 steps [ 0.0000 thru 7524.0005 ps ], 3 data sets
All averages are exact over 3762001 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Temperature 298 125.156 125.156 1.9202e-05
0.144476
Volume 126.908 53.2917 53.2917 5.61522e-06
0.0422489
Density (SI) 972.142 408.201 408.201 -4.30887e-05
-0.324199
Heat Capacity Cv: 16.9588 J/mol K (factor = 0.176389)
Isothermal Compressibility: 0.543909 /bar
Adiabatic bulk modulus: 1.83854 bar
Why am I obtaining so low density? The density seems to be constant over
that timescale.
This is my mdp file:
constraints = all-bonds
integrator = md
dt = 0.002
nsteps = 2500000
nstxout = 5000
nstvout = 50000
nstenergy = 1000
nstxtcout = 5000
energygrps = SOL
nstlist = 5
ns_type = grid
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
coulombtype = PME
fourierspacing = 0.15
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
Tcoupl = nose-hoover
tau_t = 0.1
tc-grps = SOL
ref_t = 298
Pcoupl = Parrinello-Rahman
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
pcoupltype = isotropic
gen_vel = yes
gen_temp = 298
gen_seed = -1
Thanks in advance for any help...
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
