[gmx-users] Warning: 1-4 interaction

[Justin A. Lemkul]

Moeed wrote:
> Hi everyone,
> 
> My attempt to conduct a NPT failed although everything seemed to be 
> going well. Topology is OK and I am just curious why system is blowing 
> up all of a sudden towards the end of simulation. I should mention that 
> by changing fourierspacing from 0.12 to 0.3 everything works fine till 
> the end of run and comparison between energy terms (up until the crash 
> point) shows very slight difference between two runs ( less than 2% even 
> for electrostatic terms). I am aware that blowing up is due to 
> unphysical forces but is this happening by accidient or there is an 
> underlying reason I should take care of.
> 

Everything has a cause; nothing is accidental.  No stable run should ever show 
LINCS warnings like this, so yes, there is something to fix.

You also have not proven that your fourierspacing is not the cause.  The proper 
term to analyze is Coul-recip, which corresponds to reciprocal space Coulombic 
term.  I don't see that listed below.

-Justin

> Thanks,
> Best,
> Moeed
> 
> ========================================
> step 164300, remaining runtime:   241 s          
> step 164400, remaining runtime:   240 s          
> step 164500, remaining runtime:   240 s          
> step 164600, remaining runtime:   239 s          
> Warning: 1-4 interaction between 260 and 267 at distance 73679654.990 
> which is larger than the 1-4 table size 2.250 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> =========================================
> results till t=320 ps (before first run crash)
> fourierspacing      =  0.12
> 
> LJ-14                       757.246    26.6239    26.5661 -0.0189929   
> -6.07777
> 
> Coulomb-14                 -186.509    15.9866    15.9529 -0.0112174    
> -3.5896
> 
> LJ (SR)                    -2691.84    117.026    107.231  -0.507373   
> -162.361
> 
> Coulomb (SR)                725.662    17.6483    17.5876  0.0158275    
> 5.06483
> 
>  
> 
> fourierspacing      =  0.3
> 
> 
> LJ-14                       757.129    26.4936    26.4578 -0.0149128   
> -4.77214
> 
> Coulomb-14                 -199.523     14.949     14.158 -0.0519427   
> -16.6218
> 
> LJ (SR)                     -2670.5    111.201    109.688    0.19784    
> 63.3092
> 
> Coulomb (SR)                739.794    16.1807    15.4473  0.0521352    
> 16.6834
> 
> ====================================================
> pbc              =  xyz                  
> 
>        
> ;        Run control                   
> integrator          =  md                   
> dt                  =  0.002               
> nsteps              =  1000000 ;5000         
> nstcomm             =  100               
> 
> ;        Output control
> nstenergy           =  100                  
> nstxout             =  100                 
> nstvout             =  0
> nstfout             =  0
> nstlog              =  1000                 
> nstxtcout          =  1000                 
> 
> ;        Neighbor searching
> nstlist             =  10               
> ns_type             =  grid               
> 
> ;        Electrostatics/VdW
> coulombtype         =  PME                    
> vdw-type            =  Shift             
> rcoulomb-switch     =  0                  
> rvdw-switch         =  0.9 ;0               
> 
> ;        Cut-offs
> rlist               =  1.25                 
> rcoulomb            =  1.25 ;1.1             
> rvdw                =  1.0                 
> 
> ;        PME parameters
> fourierspacing      =  0.3                 
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order          =  4                
> ewald_rtol         =  1e-5
> optimize_fft      =  yes
> 
> ;        Temperature coupling   
> Tcoupl              =  v-rescale                 
> tc-grps             =  System  ;HEX              
> tau_t               =  0.1     ;0.1                  
> ref_t               =  400     ;300             
> 
> ;        Pressure coupling
> Pcoupl              =  Parrinello-Rahman            
> Pcoupltype          =  isotropic                 
> tau_p               =  1      1           ;0.5         
> compressibility     =  4.5e-5 4.5e-5          
> ref_p               =  70    70                  
> 
> ;        Velocity generation               
> gen_vel             =  yes               
> gen_temp            =  300.0               
> gen_seed            =  173529               
> 
> ;        Bonds
> constraints             = 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

========================================