[gmx-users] Warning: 1-4 interaction

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 6 02:26:06 CET 2011



Moeed wrote:
> Hello Justin,
> 
> I just scanned through the manual and also looked into the list to learn 
> about the significance of reciprocal part to realize your statement. I 
> did not find much about the fact that how I can judge if fourierspacing 
> is the cause of the crash (I mean relevance between fourierspacing and 
> coulb recip). I suspect the cause of crashes is because of 

The manual will not describe every detail, but an understanding of the 
algorithms (through reading the appropriate literature) should provide you with 
what you need.  Take Mark's advice and leave fourierspacing at its default value 
unless you are 100% sure of the effects of messing with it.

> electrostatics settings. BEfore that I had only vdw no run crashed. 

That was a broken model, as we've discussed.  Don't believe that its results are 
reliable.

> Since I used to get LINCS warning I removed bond constraints but still 

LINCS warnings don't mean you should turn off constraints.  With a 2-fs timestep 
and an all-atom model, you absolutely need to be using constraints.

http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

> system is showing instabilities. I am confident that topology is fine 
> and just wondering how else one can inspect root cause for unphysical 
> forces.
> 

The best advice I can give has already been given:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

Watch the trajectory.  See what falls apart.

You're also applying 70 bar of pressure to a system that may not yet be properly 
equilibrated for such conditions.  I have found that the Parrinello-Rahman 
barostat is not particularly well-suited to harsh conditions, tight coupling, or 
simulations of any system that is far from equilibrium.  You might be better off 
with Berendsen (and a fairly long tau_p) until your system stabilizes.

-Justin

> 
> fourierspacing =0.12 :  Coul. recip.                636.217    
> 8.69433    8.62908  0.0167398    3.68278
> 
> fourierspacing =0.3 :    Coul. recip.                642.921    
> 6.06063    6.02832 -0.00984063   -2.16496
> 
> 
> 
> 
> 
>     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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
>     -- 
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> 
> 
> 
> -- 
> Moeed Shahamat
> Graduate Student (Materials Modeling Research Group)
> McGill University- Department of Chemical Engineering
> Montreal, Quebec H3A 2B2, Canada
> Web:http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php
> Web:http://mmrg.chemeng.mcgill.ca/
> 

-- 
========================================

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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