[gmx-users] Heating

[Carla Jamous]

Hi,
I've been using gromacs to run some tests but it's the first time I need to
heat my system very slowly, knowing that it is a quite large  system.

;
;    User spoel (236)
;    Wed Nov  3 17:12:44 1993
;    Input file
;
title               =  Yo
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
constraint_algorithm  =  Lincs
lincs_iter          =  2
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  225000    ; total 450 ps.
nstcomm             =  1
nstxout             =  250      ; collect data every 0.5 ps
nstvout             =  500     ; collect velocities every 1 ps
nstfout             =  0
nstlog              =  50
nstenergy           =  50      ; collect energies every 0.1 ps
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
coulombtype         =  PME
rcoulomb            =  0.9
vdwtype             =  cut-off
rvdw                =  1.2
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes
annealing           =  single  single
annealing_npoints   =  10      10
annealing_time      =  0 100 105 200 202 250 252 350 355 450 0 100 105 200
202 250 252 350 355 450
annealing_temp      =  50 50 100 100 150 150 200 200 300 300 50 50 100 100
150 150 200 200 300 300
; Berendsen temperature coupling is on in two groups
Tcoupl              =  Berendsen
tc-grps            =  Protein    Non-protein
tau_t               =  0.1    0.1
ref_t               =  300    300
; Energy monitoring
energygrps          =  Protein  Non-protein
; Isotropic pressure coupling is now on
Pcoupl              =  no
Pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

Please can anyone tell me if my mdp file is correct? I have a serious doubt
about gen_temp & Tcoupling.

Thanks
Carla
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