[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

[Chitrita Dutta Roy]

Hi Tsjerk,

Did you mean to send you the md.mdp file that I used to run grompp for md
simulation? I am using Gromacs 4.0.2 versision. I am not very clear about
the parameters used in mdp files. So I am sending the mdp file here.


cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002  ; ps !
nsteps              =  500000  ; total 1000 ps.
nstcomm             =  1
nstxout             =  500    ; collect data every 1 ps
nstvout             =  0
nstfout             =  0
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
vdwtype             =  Cut-off
rvdw                =  1.4
;fourierspacing    =  0.12
;fourier_nx        =  0
;fourier_ny        =  0
;fourier_nz        =  0
pme_order         =  4
;ewald_rtol        =  1e-5
;optimize_fft            =  yes
; Berendsen temperature coupling is on
Tcoupl                =  V-rescale
tau_t                 =  0.1    0.1
tc_grps               =  Protein    SOL
ref_t                 =  300        300
; Pressure coupling is on
Pcoupl              =  Parrinello-Rahman
tau_p               =  0.5
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
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