[gmx-users] Water molecule starting at atom X can not be settled; can't find a solution

[Simone Cirri]

Justin A. Lemkul wrote:

; Berendsen temperature coupling is on in three groups
> Tcoupl              =  berendsen
>
> tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+
>
> ref_t               =  300      300     300
>
> Never couple solvent and ions separately. Surely grompp warned you that you
> should be using "Protein Non-Protein"? See here:
>
> http://www.gromacs.org/Documentation/Terminology/Thermostats
>
>
Hi Justin, thanks for the suggestion. Actually, it's an error I've always
been doing and I'm glad I've solved it.
However, I'm afraid it has nothing to do with the problem, because I just
tried to run the MD again (after modifying the md.mdp as you told me) and
the fatal error is still there.
I've noticed the the T-coupling mistake is also in pr.mdp. Do you think that
correcting it and re-running the PR simulation would fix the "water molecule
can not be settled" problem?
Anyway here is the pr.mdp (as it was before):

title               =  hsacyx
warnings            =  10
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  100000    ; total 200.0 ps.
nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
coulombtype        =  PME
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing        =  0.12
fourier_nx        =  0
fourier_ny        =  0
fourier_nz        =  0
pme_order        =  6
ewald_rtol        =  1e-5
optimize_fft        =  yes
; Berendsen temperature coupling is on in four  groups
Tcoupl              =  berendsen
tau_t               =  0.1     0.1    0.1
tc-grps            =  Protein     SOL    NA+
ref_t               =  300     300    300
; Pressure coupling is on
Pcoupl              =  berendsen
pcoupltype          =  isotropic
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

Thank you

Simone Cirri
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