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

[Yi Hou]

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

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
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
>> 
>> ------------------------------------------------------------------------
>> 您可以借助 Windows Live 整理、编辑和 共享您的照片。
>> <http://www.microsoft.com/china/windows/windowslive/products/photo-gallery-ed
>> it.aspx>
>> 
>> 
>> ------------------------------------------------------------------------
>> 
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php