[gmx-users] Same one lipid in bilayer causing LINCS crashing during minimization

[Erik Henze]

Hello, I am currently attempting an energy minimization of a water+ion+DSPC
bilayer with an ion channel suspended in the bilayer. This was built using
CHARMM GUI. When I run the simulation, one lipid in particular repeatedly
keeps on causing the following error:
"Step 17, time 0.017 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

rms 0.000144, max 0.034552 (between atoms 79632 and 79634)

bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length

  79632  79634   50.2    0.1104   0.1149      0.1111

Step=   17, Dmax= 7.7e-02 nm, Epot= -1.98890e+06 Fmax= 2.83841e+04, atom=
79638



Step 18, time 0.018 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

rms 0.000361, max 0.079519 (between atoms 79638 and 79640)

bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length

  79632  79633   36.3    0.1101   0.1108      0.1111

  79632  79634   43.1    0.1149   0.1132      0.1111

  79638  79639   59.4    0.1119   0.1156      0.1111

  79638  79640   59.3    0.1113   0.1199      0.1111

Step=   18, Dmax= 9.2e-02 nm, Epot= -2.03437e+06 Fmax= 5.35800e+05, atom=
79634



Step 19, time 0.019 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

rms -nan, max 0.019185 (between atoms 79638 and 79640)

bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length

  79638  79639   33.6    0.1156   0.1121      0.1111"


and then from here it just stops.

I looked up these atoms and they correspond to one DSPC lipid which seems
unexceptional (is located away from protein, just sitting in membrane). I
tried removing the constraints in my .mdp file but this did not prevent the
EM from crashing on this same lipid. Any advice on what might be causing
this, or how to circumvent it, would be greatly appreciated, thank you!