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
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. But so was the positional restraint md, and it did not error.
Thank you,
TJ Mustard
> > > >
> > > >
> > > >
> > > > Any help would be appreciated. Also I can attach my mdp files.
> > > >
> > > >
> > > >
> > > > Thank you,
> > > >
> > > > TJ Mustard
> > > > Email: [email protected]
> > > >
> > >
> > > --
> > > ========================================
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICTAS Doctoral Scholar
> > > MILES-IGERT Trainee
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > ========================================
> > > --
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> > >
> >
> >
> >
> > TJ Mustard
> > Email: [email protected]
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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>
TJ Mustard
Email: [email protected]
TJ Mustard
Email: [email protected]
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