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

[Christopher Neale]

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!