[gmx-users] MD for DNA structure

[Urszula Uciechowska]

Dear Gromacs users,

I am trying to run MD for my DNA structure, however after typing

grompp -f nvt.mdp -c em.gor -p top -o *.tpr

I am getting an error message:

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#

NOTE 1 [file nvt.mdp]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'DNA'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Setting gen_seed to 17417
Velocities were taken from a Maxwell distribution at 310 K
Analysing residue names:
There are:    46        DNA residues
There are: 39061      Water residues
There are:   190        Ion residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...

-------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: readir.c, line: 1316

Fatal error:
Group Non-Protein not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the
'-n' option of grompp.
In that case use the '-n' option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

My nvt.mdp file contains:

 7.3.2 Preprocessing
define                  = -DPOSRES      ; defines to pass to the preprocessor

; 7.3.3 Run Control
integrator              = md                    ; md integrator
tinit                   = 0                     ; [ps] starting time for run
dt                      = 0.002                 ; [ps] time step for
integration
nsteps                  = 100000                 ; maximum number of steps
to integrate, 0.002 * 25,000 = 50 ps
comm_mode               = Linear                ; remove center of mass
translation
nstcomm                 = 1                     ; [steps] frequency of
mass motion removal
comm_grps               = Non-Protein           ; group(s) for center of
mass motion removal

; 7.3.8 Output Control
nstxout                 = 25000         ; [steps] freq to write
coordinates to trajectory
nstvout                 = 25000         ; [steps] freq to write velocities
to trajectory
nstfout                 = 25000         ; [steps] freq to write forces to
trajectory
nstlog                  = 100           ; [steps] freq to write energies
to log file
nstenergy               = 100           ; [steps] freq to write energies
to energy file
nstxtcout               = 100           ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision           = 1000          ; [real] precision to write xtc
trajectory
xtc_grps                = System        ; group(s) to write to xtc trajectory
energygrps              = System        ; group(s) to write to energy file

; 7.3.9 Neighbor Searching
nstlist                 = 1             ; [steps] freq to update neighbor
list
ns_type                 = grid          ; method of updating neighbor list
pbc                     = xyz           ; periodic boundary conditions in
all directions
rlist                   = 0.8           ; [nm] cut-off distance for the
short-range neighbor list

; 7.3.10 Electrostatics
coulombtype             = PME           ; Particle-Mesh Ewald electrostatics
rcoulomb                = 0.8           ; [nm] distance for Coulomb cut-off

; 7.3.11 VdW
vdwtype                 = cut-off       ; twin-range cut-off with rlist
where rvdw >= rlist
rvdw                    = 0.8           ; [nm] distance for LJ cut-off
DispCorr                = EnerPres      ; apply long range dispersion
corrections

; 7.3.13 Ewald
fourierspacing          = 0.12          ; [nm] grid spacing for FFT grid
when using PME
pme_order               = 4             ; interpolation order for PME, 4 =
cubic
ewald_rtol              = 1e-5          ; relative strength of
Ewald-shifted potential at rcoulomb
; 7.3.14 Temperature Coupling
tcoupl                  = berendsen                     ; temperature
coupling with Berendsen-thermostat
tc_grps                 = Non-Protein                   ; groups to couple
seperately to temperature bath
tau_t                   = 0.1                           ; [ps] time
constant for coupling
ref_t                   = 310                           ; [K] reference
temperature for coupling

; 7.3.17 Velocity Generation
gen_vel                 = yes           ; generate velocities according to
Maxwell distribution of temperature
gen_temp                = 310           ; [K] temperature for Maxwell
distribution
gen_seed                = -1            ; [integer] used to initialize
random generator for random velocities

; 7.3.18 Bonds
constraints             = all-bonds     ; convert all bonds to constraints
constraint_algorithm    = LINCS         ; LINear Constraint Solver
continuation            = no            ; no = apply constraints to the
start configuration
lincs_order             = 4             ; highest order in the expansion
of the contraint coupling matrix
lincs_iter              = 1             ; number of iterations to correct
for rotational lengthening
lincs_warnangle         = 30            ; [degrees] maximum angle that a
bond can rotate before LINCS will complain

What can be wrong? I did not have problems with energy minimization.

best regards
/Urszula




University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland


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