Moeed wrote:
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.
Your box is compressing too fast and you're violating the minimum image
convention:
http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention
I suspect you'll have to compress your system more slowly, otherwise your box
vectors are just going to crash in on your polymer chain before it has time to
adjust its configuration.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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