[gmx-users] TFE query

[Dilraj Lama]

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:dennis at iitk.ac.in,dilraj2002 at yahoo.com
mob:09415473973