[gmx-users] Fatal Error: Constraints present with Normal Mode Analysis, this combination is not supported

[Mark Abraham]

On 21/09/2011 1:38 AM, Andrey Dyachenko wrote:
> Dear gmx-users,
>
> I am trying to perform the Normal Mode Analysis of 24 kDa protein in 
> water. Here is the .mdp file I am using:
>
> integrator          = nm
> dt                  =  0.002
> nsteps              =  10000
> emtol              =  1
> nstcomm             =  1
> nstxout             =  0
> nstxtcout           =  1000
> nstvout             =  0
> nstlog              =  5000
> nstenergy           =  20
> nstlist             =  6
> ns_type             =  grid
> coulombtype         =  cut-off
> epsilon_r           =  80.0
> rcoulomb            =  1.4
> fourierspacing      =  0.12
> pmeorder            =  4
> optimize_fft        =  yes
> ewald_rtol          =  1.0e-5
> DispCorr            =  EnerPres
> constraints = none
> rlist               =  0.9
> rvdw                =  0.9
> Tcoupl              =  berendsen
> ref_t   =  330
> tc-grps             =  protein
> tau_t   =  0.5
> Pcoupl              =  no
> Pcoupltype          =  isotropic
> tau_p               =  1.0
> compressibility     =  4.5e-5
> ref_p               =  1.0
> gen_vel             =  no
> gen_temp            =  300
> gen_seed            =  1993
>
>
> And I get the error message:
>
> Fatal error:
> Constraints present with Normal Mode Analysis, this combination is not 
> supported
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> despite the constraint = none line.
>

By default, the water models include constraints. Check out the .itp 
file for your water, and you can use a define = -DWHATEVER in your .mdp 
file to choose a flexible water model. Be sure you really want (all of 
the) water present in this analysis.

Mark
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