[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.

[Justin A. Lemkul]

TJ Mustard wrote:
> 
> 
>  
> 
> 
> On January 17, 2011 at 2:15 PM TJ Mustard <mustardt at onid.orst.edu> wrote:
> 
>> No this is a completely different error that occurs when the other 
>> (EM) error does not.
>>
>>  
>>
>> 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
>> >
> 
> Quote" 
> 
> No this is a completely different error that occurs when the other (EM) 
> error does not.
> 
>  
> 
> Thank you,
> 
> TJ Mustard" end quote
> 
> I also run my steep em to an emtol of 20. This of course never happens 
> as my system converges before the emtol of 20 is reached.
> 

An Fmax of 20 is fairly stringent.  How close do you come to this target?

-Justin

> Thank you,
> TJ Mustard
> 
>  
> 
>> > >
>> > > 
>> > >
>> > > Any help would be appreciated. Also I can attach my mdp files.
>> > >
>> > > 
>> > >
>> > > Thank you,
>> > >
>> > > TJ Mustard
>> > > Email: mustardt at onid.orst.edu
>> > >
>> >
>> > --
>> > ========================================
>> >
>> > 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: mustardt at onid.orst.edu
>>
>  
> 
> TJ Mustard
> Email: mustardt at onid.orst.edu
> 

-- 
========================================

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

========================================