[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 00:48:48 CET 2011


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> wrote:
>
>> On January 17, 2011 at 2:21 PM "Justin A. Lemkul" <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> 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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