[gmx-users] Lincs warnings

[Ben Porebski]

Hi all,

I've been working on some structures between 2.5A and 3.4A in resolution
and all of my structures suffer from lincs warnings.
>From reading the page about lincs warnings, I've performed a more lengthy
equilibration:

I'm using gromacs 4.0.7 single precision and the G53a6 force field with spc
water model.

- Genbox, add ions.
- EM until converges
- Positional restraints at 2,000 kJ/mol, 200, 20 and 2 for 100ps each at
100K
- Followed by simulated annealing with the following parameters:

; Simulated annealing @ positional restraint of 2 kJ/mol
annealing = single      single
annealing_npoints   = 3           3
annealing_time = 0 50 250    0 50 250
annealing_temp = 100 100 300 100 100 300

- This then undergoes 750ps of md at 300K.

Once done. I continue the run in my production MD.
Sometimes my structures will crash within 5 ns, sometimes it will run out
for 60 ns before I start seeing any lincs warnings.

I've attempted to further refine the structures and they behave a little
better, but still crash, just less often.
To continue the simulation, I will not use the .trr output from the
previous simulation. If this doesn't work, I'll run the simulation using
shake for 2 ns, but this is significantly slower.

I'm a little concerned that these crashes may be introducing some sort of
error into the simulation and I'm not sure of the right way to get around
this problem.
I've played around with changing the lincs order and lincs iteration
parameters, which appear to reduce the number of lincs warnings and slows
down the simulation slightly.

Another thing I've played with was the constraints. Changing this from
all-bonds to hbonds.
This stopped my crashes, but a co-worker thought that it may not be
accurately modelling the system, or would introduce anomalies into the
simulation.
My impression was that changing from all-bonds to hbonds would improve the
accuracy of the system... But I could be wrong.

If anyone has experience with dealing with lincs warnings or simulating low
resolution structures, help would be amazing.
I've been stuck on this for quite some time now.


Cheers, Ben
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