On January 17, 2011 at 3:48 PM Mark Abraham <mark.abra...@anu.edu.au> wrote:
On 18/01/2011 10:27 AM, TJ Mustard wrote:
On January 17, 2011 at 2:47 PM TJ Mustard <musta...@onid.orst.edu> wrote:
On January 17, 2011 at 2:21 PM "Justin A. Lemkul" <jalem...@vt.edu> 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" <jalem...@vt.edu> 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
I have ran both light hydrogen with and without FEP on and yes the runs with the FEP give the 1-4 interaction errors. I will soon be running Heavy w/o FEP. The other very interesting part is that 108 and 116 are 17.2 Angstroms apart. They are on the same molecule(drug) but very far apart and definitely not bonded. Also my rvdw, rlist, and rcoulomb are all 0.8, which is to my knowledge 8 angstroms. How are two particles, though on the same molecule, interacting outside the PME/Cut-off distance?
And if this is a problem do I need to increase my PME/Cut-off distance such that the entire molecule is within that distance. I would rather not, due to speed issues.
Thank you,
TJ Mustard
Email: musta...@onid.orst.edu
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