Hello,
I have searched on Google for the LINCS warning problems, and there are
already many discussions,
but I guess that my situation might be different.
I have a system of protein/micelles/water_ions in a dodecahedral water
box. The system is fully equilibrated by several steps.
1. minimizations (steep, cg) with positional restraints (1000 kJ/mol
nm2) on protein and micelles,
2. 500 ps NVT equilibration, time step 1 fs, positional restraints (1000
kJ/mol nm2) on protein and micelles,
3. 500 ps NPT equilibration, time step 1 fs, positional restraints (1000
kJ/mol nm2) on protein and micelles,
4. 500 ps NPT equilibration, time step 1 fs, positional restraints (800
kJ/mol nm2) on protein and micelles,
...500 ps, restraints, 600 kJ/mol nm2, 1fs
...500 ps, restraints, 400 kJ/mol nm2, 1fs
...500 ps restraints, 200 kJ/mol nm2, 1fs
... 500 ps restraints, 100 kJ/mol nm2, 1 fs
5. 15 ns equilibration, positional restraints (100 kJ/mol nm2) only on
protein, letting the micelles assemble, time step 1 fs
6. 5 ns MD simulation, without any restraints, time step 2 fs
For all these steps, the constraints were applied to h-bonds, which is
the same for following simulations.
And the I started a Hamiltonian replica exchange simulation, 4 replicas
were chosen, time step is 2fs.
But the simulation crashed at the simulation time of 25 ns. The error is
shown like:
#
step 12855987: Water molecule starting at atom 66929 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
#
Step 12855991, time 25712 (ps) LINCS WARNING in simulation 3
relative constraint deviation after LINCS:
rms 0.000678, max 0.010615 (between atoms 3541 and 3542)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3541 3543 90.0 0.1010 0.1020 0.1010
#
Atom 3541 is ND2 of ASN227, and atom 3543 is HD22 bonded to atom 3541. I
checked the trajectory file, and I didn't find Asn227 doing something
improperly.
I also found that the constraints failure happened faster if I used 2 fs
with constraints for all bonds. I believe that a time step of 1 fs will
work, which also means
more computing time since the system is very big. Any suggestions?
Thanks very much!
All the best,
Qinghua
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
