[gmx-users] RE: RE: RE: Doubts over g_lie usage

[J Peterson]

Thank you so much for your time and explanation.

I am recalculating the energy co-ordinates and using it in g_lie
calculations.

I have read the manual and changed the .mdp file I am using. The following
is the mdp file, please check for the correctness. The text in bold font are
newly included after your suggestions. Can I use this mdp to calculate the
LIE correctly?

cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  5000000  ; total 10000 ps.
nstcomm             =  1
nstxout             =  5000
nstvout             =  5000
nstfout             =  0
nstlog              =  5000
nstenergy           =  500
nstxtcout           =  500
nstlist             =  10
ns_type             =  grid
rlist               =  1.2              ; short-range neighborlist cutoff
(in nm)
rcoulomb            =  0.9              ; short-range electrostatic cutoff
(in nm)
vdwtype             =  cut-off
rvdw                =  1.4              ; gromos96 force field/ short-range
van der Waals cutoff (in nm)
;coulombtype         =  PME             ; Particle Mesh Ewald for long-range
electrostatics
;fourierspacing      =  0.12            ; grid spacing for FFT
;fourier_nx          =  0
;fourier_ny          =  0
;fourier_nz          =  0
;pme_order           =  4
;ewald_rtol          =  1e-5
*coulombtype          =  Reaction-Field-zero
epsilon_rf           =  0*
optimize_fft        =  yes
pbc                 =  xyz
; modified Berendsen temperature coupling is on in two groups
Tcoupl              =  V-rescale        ; modified Berendsen thermostat
tc-grps             =  S04   SOL
tau_t               =  0.1   0.1
ref_t               =  300   300
; Energy monitoring
energygrps          =  S04  SOL

; Mode for center of mass motion removal
comm-mode           =  Linear
; Groups for center of mass motion removal
comm-grps           =  System

; Pressure coupling is now on
Pcoupl              =  parrinello-rahman
Pcoupltype          =  isotropic
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0

; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

~

Thanks

Peterson J



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