[gmx-users] LINCS warnings with timestep of 5 fs (but not 4 fs)

[Chris Neale]

Hello,

I am recently experimenting with a 5 fs timestep using virtual hydrogens 
and LINCS. I am getting sporadic LINCS warnings, although the system 
appears stable and does not blow up during the 100ns in which I get such 
warnings. If I reduce the timestep to 4 fs from 5 fs (and increase 
nstlist to 5 from 4), then I do not get any such LINCS warnings. It 
occurs to me that in a larger timestep there could be a larger rotation 
and that this warning may be entirely benign. I am not sure about that, 
however, and would welcome any advice here, especially on the way that 
the 30 deg threshold for a warning message is derived.

Thank you,
Chris.


Here is a snippit from my stderr output during a run:

...
Step 1387503, time 6937.51 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000156, max 0.001672 (between atoms 17832 and 17831)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  17832  17831   30.9    0.0946   0.0947      0.0945

Step 1387503, time 6937.51 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000139, max 0.001582 (between atoms 17832 and 17828)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  17832  17831   31.1    0.0946   0.0946      0.0945

Step 3601434, time 18007.2 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000035, max 0.000308 (between atoms 18168 and 18165)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  18168  18167   30.1    0.0945   0.0945      0.0945

Step 4391822, time 21959.1 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000121, max 0.002041 (between atoms 14190 and 14189)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  14190  14189   30.5    0.0945   0.0947      0.0945

Step 4796357, time 23981.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000128, max 0.001443 (between atoms 15532 and 15531)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  15532  15531   31.5    0.0945   0.0946      0.0945

Step 4796357, time 23981.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000111, max 0.001185 (between atoms 15532 and 15531)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  15532  15531   31.8    0.0945   0.0946      0.0945

Step 4796358, time 23981.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000221, max 0.002694 (between atoms 15532 and 15531)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  15532  15531   34.0    0.0946   0.0948      0.0945
...


########################################

With a .mdp file that looks like this:

integrator          =  sd
nsteps              =  20000000
tinit               =  0
dt                  =  0.005
comm_mode           =  linear
nstcomm             =  4
comm_grps           =  System
nstxout             =  20000000
nstvout             =  20000000
nstfout             =  20000000
nstlog              =  0
nstlist             =  4
nstenergy           =  20000
nstxtcout           =  20000
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  PME
rcoulomb            =  0.9
fourierspacing      =  0.12
pme_order           =  4
vdwtype             =  cut-off
rvdw_switch         =  0
rvdw                =  1.4
rlist               =  0.9
DispCorr            =  no
Pcoupl              =  Berendsen
pcoupltype          =  semiisotropic
compressibility     =  4.5e-5 4.5e-5
ref_p               =  1.     1.
tau_p               =  4.0    4.0
tcoupl              =  Berendsen
tc_grps             =  System
tau_t               =  1.0
ref_t               =  310.
ld-seed             =  -1
annealing           =  no
gen_vel             =  yes
unconstrained-start =  no
gen_temp            =  310.
gen_seed            =  -1
constraints         =  all-bonds
constraint_algorithm=  lincs
lincs-iter          =  1
lincs-order         =  6
;;;EOF