Hi Steve,
Thanks for your reply. I went back and checked the dihedral parameters and
they were correct (in agreement with the reference paper that I used). I also
tried visualizing but it was hard to infer what was going on. Shake was applied
to constrain the water molecules only.
I have been using March 23, 2008 version of LAMMPS, and after about 7000
timesteps I got the following error:
6810 437.72707 -55114.868 6950.6166 -40502.576 -13362.412
6820 540.56096 -53852.247 4716.4417 -39674.196 -8417.2828
6830 486.43893 -54796.016 5284.2222 -40997.499 -10849.766
WARNING: Dihedral problem: 5 6838 376 117 118 378
1st atom: 5 10.8197 27.1763 16.1995
2nd atom: 5 24.5555 -97.3984 55.3392
3rd atom: 5 11.1513 28.1206 14.1608
4th atom: 5 10.9582 29.2935 14.1412
:
:
:
:
WARNING: Dihedral problem: 5 6839 391 127 128 129
1st atom: 5 70.4893 32.7209 -34.5701
2nd atom: 5 -2122.74 1149.81 2015.03
3rd atom: 5 17.5977 25.1738 14.4068
4th atom: 5 9.97748 21.5286 23.1722
ERROR on proc 16: Bond atoms 129 128 missing on proc 16 at step 6840
ERROR on proc 5: Angle atoms 112 111 109 missing on proc 5 at step 6840
I Played around and tried running the same input script with an older
version of LAMMPS (June 15, 2007) and the simulation ran for 2 million timesteps
without any warning or error. Do you have any idea why this could be happening?
Here is the input script:
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/class2/coul/cut 12.0
bond_style class2
angle_style class2
dihedral_style class2
read_data data.L64_13_30_13edit
pair_coeff 1 1 0.062 3.854
pair_coeff 2 2 0.068 3.815
pair_coeff 3 3 0.120 3.3
pair_coeff 4 4 0.096 3.58
pair_coeff 5 5 0.023 2.878
pair_coeff 6 6 0.008 1.087
pair_coeff 7 7 0.0460 0.4000
pair_coeff 8 8 0.1521 3.188
pair_coeff 7 8 0.0836 1.7753
velocity all create 300 239
neighbor 2.0 bin
neigh_modify every 5 check yes
group poly molecule 1
group water molecule > 1
timestep 0.5
thermo 10
restart 1000 RS.*
fix 3 all shake 0.0001 10 0 b 5 a 8
fix 1 all nvt 300.0 300.0 100.0
dump dump_p2 poly xyz 100 dump.poly.xyz
dump dump_w2 water xyz 100 dump.water.xyz
run 2000000
Thanks for your help.
Gaurav Pranami
The dihedral warning occurs when the orientation of the 4 atoms
in the dihedral is going bad. It prints the values, so you should
be able to examine them and see it if looks bad, according
to your ff params.Are you just shaking water or H bonds in the polymer as well?
SHAKE should not give that error unless the unconstrained
positions are way off. So again this indicates something
is going badly wrong with your simulation. I would probably
try to viz things and see what is happening.Steve
> Dear LAMMPS users:
>
> I am simulating a triblock copolymer using COMPASS parameters, solvated in
> water using TIP3P and SHAKE. I have been running nvt simulations that have run
> for about 10,000 timesteps and then ended in errors with "WARNING: Dihedral
> problem" and "Shake determinant = 0.0." I have checked all of my polymer's
> parameters.
>
> I changed the command for the neigh_modify list to "every 1," to see if it's
> a neighbor list problem, but I still got dihedral errors after 12,000
timesteps.
>
> Decreasing the timestep from 0.5 to 0.05 (real units) and running for an
> equivalent period of time did not solve the error problem.
>
> I also increased the max iter. number for SHAKE from 10 to 20, but I still
> got the same errors.
>
> Additionally, simulating the polymer for about 100,000 timesteps (0.5 fs)
> without water did not give any dihedral problems.
>
> Any help in this matter would be appreciated. If needed, I can attach my
> input and data files.
>
> Thanks
>
>
> Gaurav Pranami
>
> Graduate Student
> Chemical Engineering Dept.
> Iowa State University
>
>
>
>
>
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Gaurav Pranami
Graduate Student
Chemical Engineering Dept.
Iowa State University