[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
below:
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
directions
; 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=
nsteps*dt
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
steps
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/rvdw
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
coupling
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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