[gmx-users] warming up a protein system

morpheus morpheus.sommer2008 at gmail.com
Mon Jul 9 10:55:30 CEST 2018

Dear Gromacs users,

I have a few questions about the warming-up procedure of a simple ~600AA
protein in water using the Gromos force field and SPC water. First I do an
energy minimization and then I want to warm my protein up to 310K.

1) What does the "constraints =  all-bonds" mean exactly? In the manual I
just found a cryptic "Convert all bonds to constraints." I read elsewhere
that this is needed if "detail of bonds' oscillation is not important". But
what is really done here? Is the length of bonds unchangeable (very
difficult to change) or also their angle?

2) Is it ok to not generate velocities during the warm-up and do it for the
production runs only? ("gen_vel =  no"). I saw that the default for
"gen_temp" is 300K so it would run until 300K without and then generate the
velocities? Because generating velocities close to 0 Kelvin possibly does
not make much sense? So is it better not to generate them in the warm-up at

The full mdp file is given below.

I would really like to fully understand what is happening here and which
parameterizations make sense ...

Thanks for your help!

title               =  PR
cpp                 =  /lib/cpp
define              =  -DPOSRES        ; defines to pass to the
preprocessor: Will tell grompp to include posre.itp into your topology,
used for position restraints.
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ;

nsteps              =  250000 ; 500 ps of warming-up

nstxout                  = 0            ; frequency to write coordinates to
output trajectory file [steps]
nstxtcout                = 500         ; frequency to write coordinates to
xtc trajectory [steps]
xtc_grps                 = SYSTEM;  ; which groups to write to xtc file
xtc-precision            = 1000     ; precision to write to xtc trajectory
nstvout                  = 0        ; frequency to write velocities to
output trajectory file  [steps]
nstfout                  = 0     ; frequency to write forces to output
trajectory file      [steps]
nstlog                   = 0     ; frequency to write energies to log file
nstenergy                = 0     ; frequency to write energies to energy
file [steps]

nstlist             =  10
ns_type             =  grid
rlist            =  1.4

coulombtype        =  PME
rvdw            =  1.4
rcoulomb        =  1.4
fourierspacing        =  0.12
pme_order        =  4
ewald_rtol        =  1.0e-5
optimize_fft        =  yes

; Berendsen temperature coupling is on in two groups
Tcoupl              =  V-rescale
tc_grps            =  Protein    Non-Protein
tau_t               =  0.1    0.1
ref_t               =  310    310

; Simulated Annealing
annealing           =  single    single        ; A single sequence of
annealing points
annealing_npoints   =  2    2                ; A list with the number of
annealing control points used for each temperature group
annealing_time      =  0 80    0 80            ; List of times at the
annealing control points for each group
annealing_temp      =  0 310    0 310        ; List of temperatures at the
annealing control points for each group

; Energy monitoring
energygrps        =  Protein    SOL

; Isotropic pressure coupling is on
Pcoupl              =  berendsen
Pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0

refcoord-scaling = all ; The reference coordinates are scaled with the
scaling matrix of the pressure coupling.

; Generate velocites is off.
gen_vel             =  no

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