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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