[gmx-users] 1-4 interaction at distance larger than 1

[Justin A. Lemkul]

houyi wrote:
> Dear all,
> I guess others have the same problem for me as well, and it may repeat 
> to ask it again due to i am new for gromacs- 3.3.3. my protein is 
> 1z92.pdb. when i perform the energy minimization , i got this error. but 
> when i used for another small protein, which is 1ycr.pdb, it worked well 
> for all. i choose the OPLS-AA/L all-atom force field
> my em.mdp is
> title               =  protein
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  100
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                = 1.0
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1000.0
> emstep              =  0.01
> 
> i found the website and some one said change the table extension to 2 or 
> 3 or maybe more, it works for this step, but after performing the 
> postion constrains, it got the wrong results. so i guess i will not 
> change the table extension, and i do not why it only work for small 
> protein not for larger one, and i repeated sevel times, such as changing 
> timesteps and rlist and rcoulomb and rvdw to 0.9. still not working. 
> could anyone help me to explain this.

Your system is blowing up due to some non-physical interaction.  Tweaking the 
table-extension is probably not going to help.  Some general references:

http://oldwiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off

http://oldwiki.gromacs.org/index.php/blowing_up

Without knowing more about how you prepared the system (exact commands), then 
you will not likely get much more useful advice.  Take a look at where things 
are falling apart (atom numbers printed in the .log file) and see if you can 
deduce the source of the problem.

-Justin

> thank you very much
> Reards,
> Yi
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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