[gmx-users] grompp error-box vectors

[Justin A. Lemkul]

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
> 

-- 
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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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