Re: [gmx-users] 9 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.

[Justin A. Lemkul]

ajani haresh wrote:
 

 

Respected Sir,

 

 

Myself Haresh  Ajani from National Institute of Pharmaceutical Education 
& Research.

 

I am using gromacs version 4.5.3. I am working on molded Protein.

 

I am facing one problem in gromacs after minimization of the protein.

 

I have put my query here.

 

 

Fatal Error : Wrote pdb files with previous and current coordinates

 

Warning: 1-4 interaction between 687 and 691 at distance 4.001 which is 
larger than the 1-4 table size 2.000 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

 

Fatal error:

 

9 particles communicated to PME node 5 are more than 2/3 times the 
cut-off out of the domain decomposition cell of their charge group in 
dimension x.

 

This usually means that your system is not well equilibrated.

 

 

I have given run for gromacs.

 

Pdb2gmx -f 1.pdb -o 12.pdb -p 12.top -ignh -ter -missing

then I have selected gromos force field and SPC water model.

 

editconf -bt cubic -f 12.pdb -o 123.pdb -c -d 0.9

 

genbox -cp 123.pdb -cs spc216.gro -p 123.top -o 123_b4ion.pdb

 

 then neutralize the protein and  energy minimization.

 

 

 

 

Steepest Descents:

 

   Tolerance (Fmax)   =  1.00000e+03

 

   Number of steps    =         3500

 

 

 

writing lowest energy coordinates.

 

 

 

Steepest Descents converged to Fmax < 1000 in 3468 steps

 

Potential Energy  = -9.6223600e+05

 

Maximum force     =  9.3264703e+02 on atom 695

 

Norm of force     =  2.5498827e+01

 

 

 

Step 0, time 0 (ps)  LINCS WARNING


The outcome of energy minimization seems reasonable, but the fact that the 
system instantly explodes suggests that there is still something physically 
unreasonable in (1) your .mdp file or (2) the coordinates of the system.

http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

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

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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