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

[Andrey Dyachenko]

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.

I am using GROMACS 4.5.4

Any suggestions will be very welcomed

Thanks!


-- 
Andrey Dyachenko
PhD Student

Design, structure and synthesis of peptides and proteins
Institute for Research in Biomedicine (IRB Barcelona)
C/Baldiri i Reixac 10-12
08028 Barcelona
Tel: +34 93 403 71 27
Fax: +34 93 403 71 26
www.irbbarcelona.org
www.pcb.ub.es/giralt/html/home.html
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