On 18/01/2011 10:27 AM, TJ Mustard wrote:
On January 17, 2011 at 2:47 PM TJ Mustard <[email protected]> wrote:
On January 17, 2011 at 2:21 PM "Justin A. Lemkul" <[email protected]>
wrote:
>
>
> TJ Mustard wrote:
> >
> >
> > No this is a completely different error that occurs when the
other (EM)
> > error does not.
> >
>
> So, EM completes, but you then get this unstable system? How well
did EM
> converge? Were the potential and maximum force acceptable?
>
> Instabilities are generally caused by incorrect topologies or .mdp
settings.
> Those are the first places I would look for sources of error.
>
> -Justin
>
> >
> >
> > Thank you,
> >
> > TJ Mustard
> >
> > On January 17, 2011 at 1:51 PM "Justin A. Lemkul"
<[email protected]> wrote:
> >
> > >
> > >
> > > TJ Mustard wrote:
> > > >
> > > >
> > > > Hi all,
> > > >
> > > >
> > > >
> > > > We have been running a lot of simulations on protein ligand
> > > > interactions, and my settings/setup/mdp files worked great
for one
> > > > system. Then when we moved to a larger and more complicated
system we
> > > > started getting mdrun 1-4 interaction errors in our MD.
> > > >
> > > >
> > > >
> > > > We are running with heavyh and have correctly made our
ligands with
> > > > acpype and edited to have heavyh.
> > > >
> > > > Same setup as our smaller simpler model, but keep getting these:
> > > >
> > > >
> > > >
> > > > Warning: 1-4 interaction between X and Y at distance 1.804
which is
> > > > larger than 1-4 table size 1.800 nm.
> > > >
> > > >
> > > >
> > > > The jobs will continue on and finish but we are worried about
the error
> > > > that could be included with these errors.
> > > >
> > > >
> > >
> > > Is this related to the other issue we're discussing? If so, please
> > do not
> > > double-post, especially if you're including different
information in
> > different
> > > threads. It becomes a nightmare to try to keep track of.
> > >
> > > That particular error is usually not a good sign. Normal, stable
> > simulations
> > > should not give such an error.
> > >
> > > -Justin
> > >
Here is the tail of my em:
Step= 3438, Dmax= 2.5e-04 nm, Epot= -1.05878e+06 Fmax= 8.91784e+01,
atom= 43563
Step= 3439, Dmax= 3.0e-04 nm, Epot= -1.05878e+06 Fmax= 8.89898e+01,
atom= 43563
Step= 3440, Dmax= 3.6e-04 nm, Epot= -1.05878e+06 Fmax= 3.27390e+02,
atom= 24
Step= 3441, Dmax= 4.3e-04 nm, Epot= -1.05878e+06 Fmax= 3.34235e+02,
atom= 24
Step= 3451, Dmax= 1.0e-06 nm, Epot= -1.05878e+06 Fmax= 3.32604e+02,
atom= 24563
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 20
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 3452 steps,
but did not reach the requested Fmax < 20.
Potential Energy = -1.0587850e+06
Maximum force = 3.3423511e+02 on atom 24
Norm of force = 4.9464898e+00
My major settings are:
define = -DPOSRES_WATER
integrator = steep
nsteps = 10000
emtol = 20
emstep = 0.01
Am I setting my emtol to low? I occasionally see a Fmax of ~250-900
but mostly above that.
I am currently having the epiphany that -DPOSRES_WATER could be my
problem.
Thank you,
TJ Mustard
OK I ran the EM without the -DPOSRES_WATER defined and continued
through my script to pr and md, and I got this error on my first MD
after a positional restraint md (we call it a PR).
First the EM tail:
Step= 5519, Dmax= 8.3e-04 nm, Epot= -1.09261e+06 Fmax= 8.13679e+02,
atom= 24
Step= 5520, Dmax= 1.0e-03 nm, Epot= -1.09261e+06 Fmax= 7.21335e+02,
atom= 24
Step= 5523, Dmax= 3.0e-04 nm, Epot= -1.09261e+06 Fmax= 2.58642e+02,
atom= 24
Step= 5527, Dmax= 4.5e-05 nm, Epot= -1.09261e+06 Fmax= 1.88718e+02,
atom= 24936
Step= 5533, Dmax= 1.7e-06 nm, Epot= -1.09261e+06 Fmax= 1.86052e+02,
atom= 24
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 20
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 5534 steps,
but did not reach the requested Fmax < 20.
Potential Energy = -1.0926141e+06
Maximum force = 1.8871829e+02 on atom 24
Norm of force = 4.8353853e+00
That looks fine.
Now the MD tail:
No previous checkpoint file present, assuming this is a new run.
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file RFP-t_md.tpr, VERSION 4.5.3 (single precision)
Starting 2 threads
Loaded with Money
Making 1D domain decomposition 2 x 1 x 1
starting mdrun 'ligand in water'
25000 steps, 100.0 ps.
step 10400, will finish Mon Jan 17 15:51:43 2011Warning: 1-4
interaction between 108 and 116 at distance 1.800 which is larger than
the 1-4 table size 1.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
step 11700, will finish Mon Jan 17 15:52:10 2011imb F 0%
Any thoughts? Remember this system is doing FEP and heavy hydrogens.
Simplify things while troubleshooting. Does normal MD work instead of
FEP? Do normal hydrogens work?
Use nstxout = 1 and look and the region around atoms 108 116 to see what
is breaking. That may tell you why it is breaking.
But so was the positional restraint md, and it did not error.
Shrug, numerical instabilities can take time to show up.
Mark
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