[gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!

[Mark Abraham]

On 11/11/2010 3:14 AM, Miguel Machuqueiro wrote:
>
> Dear users and developers,
>
> In GROMACS 4.5.x when using "freeze groups" on a Protein in a 
> Protein+Solvent system, I noticed that the coordinates of a few atoms 
> (not many, but a few) are changed after a short period of MD (~0.2 
> ps). Of course, this is wrong!
>
> Are there any options in MDP/GROMPP/MDRUN that can be originating 
> this? Or it is some bug in the code?
>
> A copy of my input file follows below.
>
> Note that this version of GROMACS crashes if one uses "constraints" in 
> LINCS together with "freeze groups". Hence the "constraints = none" line.

Indeed, because imposing the constraints can perturb the (frozen) 
positions slightly, leading to numerical issues... Similarly, if you 
couple the frozen groups to a heat bath, you're going to find that 
they're not actually frozen. And pressure-coupling is not known to 
always play nicely with frozen groups either (search the archive for more).

>
> Any help is appreciated.
>
> Regards,
> Miguel
>
> _____________
>
> ;       Input file
> ;
> title               =  zzz
> cpp                 =  /lib/cpp
> define              =
>
> integrator          =  md
> tinit               =  0.0
> dt                  =  0.002    ; ps !
> nsteps              =  100
> nstcomm             =  10
> nstxtcout           =  500
> xtc-precision       =  1000
> nstxout             =  0
> nstvout             =  0
> nstfout             =  0
> nstlog              =  0
> nstenergy           =  500
> nstcalcenergy       =  10
> ns_type             =  grid
>
> coulombtype         = Generalized-Reaction-Field
> nstlist             =  5
> rlist               =  0.8
> rcoulomb            = 1.4
> epsilon_rf          = 54.0
> rvdw                = 1.4
>
> vdwtype             = cut-off
>
> ; Energy monitoring
> energygrps          =  Protein SOL
>
> Tcoupl              =  v-rescale
> tc-grps             =  Protein   SOL
> tau_t               =  0.10      0.10
> ref_t               =  310.0     310.0
>
> ; Isotropic pressure coupling is now on
> Pcoupl              =  berendsen
> Pcoupltype          =  isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
>
> ; lincs_order value of 8 works better than 4
> constraint_algorithm=lincs
> lincs_order         =  8
> constraints         =  none
> lincs-warnangle     =  90
>
> freezegrps          =  Protein
> freezedim           =  Y Y Y
> energygrp_excl      =  Protein Protein
>
>