[gmx-users] grompp error-box vectors

Moeed lecielll at googlemail.com
Sun Aug 1 01:04:32 CEST 2010

Dear gmx users,

I am trying to compress a single polymer chain. grompp is giving the error

Program mdrun, VERSION 4.0.7
Source code file: ns.c, line: 2299

Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.

I dont realize the error exactly...I tried compressing with different ref
pressures of 30 10 and 1 bar.. can you please guideme whre the problem lies.

Actually later I will have to work with much longer chains so this
compressing issue can become even more challanging. I wanted to know how I
can decide on P coupling parameters (tau_P, pcoupling type or even coupling
algorithm ..) when it comes to compressing different chain lengths and
different number of chains in the box...

Thank you,

pbc              =  xyz                   ; use priodic BCs in all

;        Run control
integrator          =  md                 ; type of dynamics algorithm. Here
md uses a leap-frog algorithm for integrating Newtons's eq of motion
dt                  =  0.001                 ; in ps !
nsteps              =  4000000              ; length of simulation=
nstcomm             =  1                 ; frequency for center of mass
motion removal

;        Output control
nstenergy           =  100                  ; frequency to write energies to
energy file. i.e., energies and other statistical data are stored every 10
nstxout             =  100                 ; frequency to write
coordinates/velocity/force to output trajectory file. how often snapshots
are collected= nstxout*dt
nstvout             =  0
nstfout             =  0
nstlog              =  1000                 ; frequency to write energies to
log file
nstxtcout          =  0                 ; frequency to write coordinates to
xtc trajectory

;        Neighbor searching
nstlist             =  10                 ; frequency to update neighbor
list. Neighborlist will be updated at least every 10 steps. Manual p80
ns_type             =  grid                 ; make a grid in the box and
only check atoms in neighboring grid cells when constructing a new neighbor
list every nstlist steps

;        Electrostatics/VdW
;coulombtype         =  PME                      ; tells gromacs how to
model electrostatics. Shift: Coulomb/LJ potential is decreased over the
whole range and forces decay smoothly to zero between
vdw-type            =  Shift               ; rcoulomb-switch/rvw-switch &
rcoulomb-switch     =  0                    ; where to start switching the
Coulomb potential
rvdw-switch         =  0.9 ;0                 ; where to start switching the
LJ potential

;        Cut-offs
rlist               =  1.1                 ; in nm. Cut-off distance for
short-range neighbor list
rcoulomb            =  1.1 ;1.0             ; distance for coulomb cut-off
rvdw                =  1.0                 ; distance for coulomb cut-off

;        Temperature coupling
Tcoupl              =  v-rescale        ;berendsen
tc-grps             =  System  ;HEX               ; groups to couple to
thermostat; Berendsen temperature coupling is on in these groups
tau_t               =  0.1     ;0.1               ; time constant for T
ref_t               =  300     ;300               ; reference T for
coupling. When you alter the T, don't forget to change the gen_temp for
velocity generation

;        Pressure coupling
Pcoupl              =  Parrinello-Rahman;berendsen
Pcoupltype          =  semiisotropic    ;isotropic ; isotropic: means the
box expands and contracts in all directions(x,y,z)in order to maintain the
proper pressure;semiisotropic: isotropic in x & y directions
tau_p               =  1      1           ;0.5       ; time constant for
coupling in ps
compressibility     =  4.5e-5 4.5e-5           ; compressibility of solvent
used in simulation in 1/bar
ref_p               =  1.0    1.0               ; reference P for coupling
in bar

;        Velocity generation               Generate velocites is on at 300
K. Manual p155
gen_vel             =  yes                 ; generate velocites according to
Maxwell distribution at T: gen_temp with random gen seed gen_seed
gen_temp            =  300.0                 ; T for Maxwell distribution
gen_seed            =  173529                 ; used to initialize random
generator for random velocities

;        Bonds
constraints         =  none ;all-bonds           ; sets the LINCS constraint
for all bonds
constraint-algorithm = lincs
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