Hello gmx users,
I have a query and would be greatfull if I could get some
suggestions on the subject.
I constructed a "tfe.itp" file with the
parameters mentioned by Fioroni et. al., J.
Phys. Chem. B 2000, 104, 12347-12354. I then
generated a "tfe.gro" file using InisghtII
molecular modeling package followed by
genconf.
I ran a "energy minimization" fand then a 2ns NPT ensemble Molecular
Dynamics simulation on the system.
My Parameter file is as follows:
--------------------------------------------
title = equilibration
cpp = /lib/cpp
integrator = md
dt = 0.002 ; ps !
nsteps = 1000000 ; total 2ns
nstcomm = 1
nstxout = 500
nstvout = 50000
nstfout = 0
nstxtcout = 500
xtc_precision = 1000
nstlog = 100
nstenergy = 100
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 0.8
rcoulomb = 1.4
rvdw = 1.4
; Berendsen temperature coupling is on
Tcoupl = berendsen
tau_t = 0.1
tc-grps = TFE
ref_t = 300
energygrps = TFE
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 4.0
compressibility = 1.22e-4
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
--------------------------------------------
I did not specify "Lincs algorithm" in the parameter file to constrian the
bonds, rather I used [constraints] for bond distance in the "tfe.itp" file
itself.
I tried using tau_p as 1ps to 3 ps, but in doing so, my simulation crashed
after a certain period with the error message as "high pressure scaling,
and the failure of the constraint algorithm (either lincs or shake)".
So I used tau_p as 4 ps which is the value used for simulation in the
paper mentioned above.
The isothermal compressibility for liquid TFE at 298K is 1.22e-4
The density of TFE at 298K is 1383 Kg/m3.
These values are mentioned in the paper.
I then calculated the Properties "Temperature, pressure and density" for
the simulation using "g_energy".The average vaules for the properties are
as:
Temperature: 300.67
Density: 1402.95
Pressure: -2.59
Is the density value reasonable???
Why is the pressure value so different?????
I would be very greatfull If I could get some suggestions on the
parameters and on the values of the properties mentioned.
Thank you.
--
Dilraj Lama,
Graduate student,
Bioinformatics and Biomolecular Simualtion lab,
Dept. of BSBE;IITK-kanpur,
Uttar pradesh,India-208016.
email:[EMAIL PROTECTED],[EMAIL PROTECTED]
mob:09415473973
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