[gmx-users] warming up a protein system

[Justin Lemkul]

On 7/9/18 4:55 AM, morpheus wrote:
> 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

It means the bond lengths of all bonds are fixed at their equilibrium 
values.

> 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?

Angles are not affected by constraints unless you ask for "constraints = 
all-angles" (very unusual).

>
> 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
> all?

If you're warming from zero, it shouldn't really matter because all 
velocities would be zero anyway. When using annealing options, most of 
the standard thermostat settings are ignored by necessity, anyway.

-Justin

> 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!
> M
>
>
>
>
>
> 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
> [real]
> 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
> [steps]
> 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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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