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

[Justin A. Lemkul]

Yi Hou wrote:
> Dear Justin 
> Thank you very much
> My commands are:
> 1. add hydrogens, get top and gro files
> pdb2gmx -f 1z92.pdb -o 1z92.gro -p 1z92.top
> 

If I'm not mistaken, 1z92 has substantial stretches of missing residues, and you 
probably had to model them in.  I'd look at those regions as being potentially 
problematic.

> 2. specify the box size, and add water to the system
> editconf -f 1z92.gro -bt cubic -d 0.7 -o box.gro
> genbox -cp box.gro -cs spc216.gro -p 1z92.top -o sol.gro
> 
> 3. grommpp -f em.mdp -p 1z92.top -c sol.gro -o em.tpr then found the system
> is charge -3
> 
> 4. add 3NA+ ions in the SOL system
> genion -s em.tpr -p 1z92.tpr -p 1z92.top -o sol_ion.gro -pname NA+ -np 3
> -nname CL- -nn 0 -random
> 
> 5. perform the energy minimization simulation
> grompp -f em.mdp -p 1z92.top -o sol_ion.gro -o em.tpr
> mdrun -deffnm em -v
> 
> Those commands until now then I should do position constraints and equil
> simulations with my pr.mdp and md.mdp parameters.
> I will check my .log file again to see if any errors occur

I'd stop and diagnose why the minimization failed.  If you can't finish EM, 
there is no point in running any sort of dynamics, equilibration or otherwise.

-Justin

> Thank you very much
> Yi
> 
> 
> On 03/08/2009 15:56, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> 
>>
>> 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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> 
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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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