[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Jan 18 21:50:37 CET 2011
On 19/01/2011 7:33 AM, TJ Mustard wrote:
>
>
> On January 17, 2011 at 3:48 PM Mark Abraham <Mark.Abraham at anu.edu.au>
> wrote:
>
>> On 18/01/2011 10:27 AM, TJ Mustard wrote:
>>>
>>>
>>> On January 17, 2011 at 2:47 PM TJ Mustard <mustardt at onid.orst.edu>
>>> <mailto:mustardt at onid.orst.edu> wrote:
>>>
>>>> On January 17, 2011 at 2:21 PM "Justin A. Lemkul" <jalemkul at vt.edu>
>>>> <mailto:jalemkul at 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"
>>>> <jalemkul at vt.edu> <mailto:jalemkul at 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.
>
Something's impossible there. 1-4 interactions can arise only when three
bonds connect the atoms. What's your drug topology?
> 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?
>
1-4 interactions have nothing to do with PME or cut-offs. See manual 4.6.1.
Also, such short cut-offs need compensating changes in ewald_rtol and
fourier_spacing. 1.0nm with 1e-5 and 0.12nm are normal, well-tested values.
>
> 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.
>
Certainly not, even if it was relevant :-)
Mark
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