[gmx-users] default -rdd with distance restraints seems too large

Thu Oct 17 18:47:31 CEST 2013

Hi Chris,

I mentioned that PS would have helped! I am sorry about the confusion. I should have been more clear. I guess you have not followed the particle decomposition threads lately :)) 

The PD option has been associated some serious issues lately … notably I noticed it does not work well in combination of REMD. Some info is not communicated correctly and thus a few variables are wrong. I forgot which ones … 

Most recently Floris (a PhD student with us in Groningen) has noticed that turning PD on would lead to severe buckling of a membrane to the point that the system would crash. The is happening quite fast. 

If you can use an older version of GMX (4.0.7) this would be fine but starting 4.5.5 things are ugly :))

I hope this helps.

On Oct 17, 2013, at 5:57 PM, Christopher Neale <chris.neale at mail.utoronto.ca> wrote:

> Thanks for the hint XAvier.
> 
> Unfortunately, I get crashes with particle decomposition (see below). If I use either DD or PD, I can run on up to 2 threads 
> without adjusting -rdd or -dds. I can only use >2 thread with DD if I set -rdd 2.8. If I try to use more than 2 threads with PD, 
> I get lincs problems and immediate crashes. If I export GMX_MAXCONSTRWARN=-1 with the same setup , then I get a segfault immediately. 
> Note, however, that if I use constraints=none and set my timestep to 0.5 fs, I can indeed use PD with 8 threads (without exporting GMX_MAXCONSTRWARN). 
> Also note that I am using the SD integrator, but I just tested and PD also gives me an error with the md integrator.
> (( I don't think that the crashes have anything to do with improper setup. These runs are fine in serial or in parallel as described 
> above and only ever "explode"/crash with PD and >2 threads, for which they do so immediately )).
> 
> Here is the error that I get when I 
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS: 
> rms 218.843810, max 8135.581543 (between atoms 15623 and 15624)
> bonds that rotated more than 30 degrees: 
> atom 1 atom 2  angle  previous, current, constraint length
>  13908  13916   90.8    0.2130   0.8066      0.1538 
>  13916  13917   90.3    0.2402   0.7979      0.1111 
>  13916  13918   90.2    0.2403   0.8452      0.1111
>  13916  13919   89.3    1.3408   0.9956      0.1430
> ...
> ...
>  22587  22589   31.7    0.4648   0.1144      0.1111
>  22587  22590   90.2    0.4168   0.1273      0.1111
> 
> Wrote pdb files with previous and current coordinates
> starting mdrun 'Gallium Rubidium Oxygen Manganese Argon Carbon Silicon in water'
> 5000000 steps,  10000.0 ps.
> 
> WARNING: Listed nonbonded interaction between particles 13908 and 13920
> at distance 3f which is larger than the table limit 3f nm.
> 
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
> 
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
> 
> 
> 
> step 0: Water molecule starting at atom 39302 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> 
> step 0: Water molecule starting at atom 53072 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 2569455308.447471, max 215672291328.000000 (between atoms 14054 and 14055)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>  13442  13444   90.0    0.1111   0.1147      0.1111
>  13503  13506   40.8    0.1538   0.2002      0.1538
>  13506  13507   45.2    0.1111   0.1541      0.1111
> ...
> ...
>  19020  19023   89.8    0.1534 66420.9531      0.1530
> ;;dispcorr = EnerPres  ;; not using for CHARMM simulations
> 
> 
> ###########################################################
> 
> mdp options:
> 
> constraints = all-bonds
> lincs-iter =  1
> lincs-order =  6
> constraint_algorithm =  lincs
> integrator = sd
> dt = 0.002
> tinit = 0
> nsteps = 5000000
> nstcomm = 1
> nstxout = 5000000
> nstvout = 5000000
> nstfout = 5000000
> nstxtcout = 500
> nstenergy = 500
> nstlist = 10
> nstlog=0 ; reduce log file size
> ns_type = grid
> vdwtype = switch
> rlist = 1.2
> rlistlong = 1.3
> rvdw = 1.2
> rvdw-switch = 0.8
> rcoulomb = 1.2
> coulombtype = PME
> ewald-rtol = 1e-5
> optimize_fft = yes
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> tc_grps             =  System           
> tau_t               =  1.0               
> ld_seed             =  -1               
> ref_t = 310
> gen_temp = 310
> gen_vel = yes
> unconstrained_start = no
> gen_seed = -1
> Pcoupl = berendsen
> pcoupltype = semiisotropic
> tau_p = 4 4
> compressibility = 4.5e-5 4.5e-5
> ref_p = 1.0 1.0
> disre = simple
> disre-fc = 5
> 
> 
> -- original message --
> 
> Yes it is a pity!
> 
> But particle decomposition helps :)) well helped!
> 
> --
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