[gmx-users] A question on LINCS error after significant simulation time around 400ps.

[Hwankyu Lee]

Dear, gmx-users,

I'm running peptide(SP-B(1-25),including aromatics) simulations with monolayers.
I put peptide, which is used with "-dummy hydrogens" option, into monolayers
with different angles with respect to interface between water and monolayers,
and then I got LINCS error from one of them around 400ps, although other
simulations were running nicely until 500ps.

I would like to know why this error happen after significant simulation time
(100ps). The simulation was running until 400ps, and then LINCS error suddenly
shows up, saying there is over 30 degrees with some atoms, especially
aromatics. If aromatics caused this problem, other systems with different
peptide angles with respect to interface should also get errors, but they
didn't...
Basically, when I tried to use "-dummy aromatics", I could see LINCS errors all
the time, therefore I chose "-dummy hydrogens" for my peptide including
aromatics, and then I witnessed that it worked... Therefore, I would like to
know why this error shows up suddenly around 400ps, and even in only one system
although only difference among them is different angle between peptide and
interface of monolayers and water.

this is the errors I got..
-----------------------------
Step 62302, time 311.51 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.046680 (between atoms 65 and 66) rms 0.002679
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     66     70   43.4    0.1390   0.1359      0.1390
     68     72   44.3    0.1392   0.1361      0.1390

Step 62304, time 311.52 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 34.410912 (between atoms 68 and 72) rms 0.851489
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     59     61   41.8    0.1331   0.1889      0.1330
     61     63   82.8    0.1472   0.3231      0.1470
     63     64   85.4    0.1534   0.4574      0.1530
     63     77   74.7    0.1532   0.2986      0.1530
     64     65   80.6    0.1531   0.9578      0.1530
     65     66   70.6    0.1387   1.3949      0.1390
     65     68   96.6    0.1418   4.0402      0.1390
     66     70   83.5    0.1388   4.7377      0.1390
     68     72   83.6    0.1389   4.9221      0.1390
     70     74   96.5    0.1407   4.0321      0.1390
     72     74   70.3    0.1381   1.6808      0.1390
     74     75   85.7    0.1361   1.0836      0.1360
     74     76  111.4    0.1952   1.4493      0.1985
----------------


best,
Hwankyu.