Hi,
Attached is the data file with this email. I am looking at the formation of
micelles and this is the smallest system that I have tried.
I did try running the polymer chain alone (without water) for 200,000
timesteps with a timestep of 0.5 fs. I got no dihedral warning or error using
the March 23 version of LAMMPS. When I added water (TIP3P), I got the errors
that I reported earlier. However, using 15 June version I got no error or
warning for any system.
Thanks
Gaurav
If you look at the first warning:
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 14.1412the system has already blown up. These coords
are spaced far apart. So the question is why this
is happening. I don't recall any changes to
class 2 ff or SHAKE in the last year, so it's puzzling
that it ran further in an earlier version of LAMMPS.Can you send me your data file. Also, can you see
if you can reproduce this behavior with a small system?Steve
> 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
>
>
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
> Don't miss this year's exciting event. There's still time to save $100.
> Use priority code J8TL2D2.
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>
Gaurav Pranami
Graduate Student
Chemical Engineering Dept.
Iowa State University
data.L64_13_30_13edit (587 KB)