[gmx-users] Slab Ewald test

[Justin A. Lemkul]

Alex Marshall wrote:
> Hi all,
> 
> I'm currently trying to run a simple test on how electrostatics are 
> handled in gromacs when the slab Ewald summation is used. My system 
> consists of 26 point charges, with 25 arranged in a square lattice in 
> the XY plane and the 26th above the charge in the middle. My goal is to 
> calculate the force on the particle above and the total electrostatic 
> energy. I have written my own coordinate and topology files, and they 
> grompp just fine, but when I try to mdrun for just one step, I get a 
> segfault. Trajectory files are still produced, but when I try to have 
> trjconv output the forces, it just writes the coordinates. The command I 
> used was:
> trjconv -f traj.trr -s topol.tpr -n index.ndx -novel -force -o results.gro

The better method for writing forces is g_traj.  There is no field in the output 
.gro file for forces, so you won't get them as output from trjconv.  The -force 
flag is there likely so that .trr files can be read and written, but it has no 
application to other file formats.

> I've set nxtxout, nxtvout and nxtfout to 1 in my mdp file, so if not for 
> the segfault, I believe I should have force data. How can I fix the 
> segfault?
> 

A seg fault means that your system has become unstable.  In general:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

> .itp file for charges:
> [ moleculetype ] ; Name nrexcl CHR 3 [ atoms ] ; nr type resnr residue 
> atom cgnr charge mass typeB chargeB massB 1 H 1 CHR H3 1 1 1 H 0 0 ; 
> qtot 0 2 H 1 CHR H6 2 -1 1 H 0 0 ; qtot 0 3 H 2 CHR H3 3 1 1 H 0 0 ; 
> qtot 0 4 H 2 CHR H6 4 -1 1 H 0 0 ; qtot 0 5 H 3 CHR H3 5 1 1 H 0 0 ; 
> qtot 0 6 H 3 CHR H6 6 -1 1 H 0 0 ; qtot 0 7 H 4 CHR H3 7 1 1 H 0 0 ; 
> qtot 0 8 H 4 CHR H6 8 -1 1 H 0 0 ; qtot 0 9 H 5 CHR H3 9 1 1 H 0 0 ; 
> qtot 0 10 H 5 CHR H6 10 -1 1 H 0 0 ; qtot 0 11 H 6 CHR H3 11 1 1 H 0 0 ; 
> qtot 0 12 H 6 CHR H6 12 -1 1 H 0 0 ; qtot 0 13 H 7 CHR H3 13 1 1 H 0 0 ; 
> qtot 0 14 H 7 CHR H6 14 -1 1 H 0 0 ; qtot 0 15 H 8 CHR H3 15 1 1 H 0 0 ; 
> qtot 0 16 H 8 CHR H6 16 -1 1 H 0 0 ; qtot 0 17 H 9 CHR H3 17 1 1 H 0 0 ; 
> qtot 0 18 H 9 CHR H6 18 -1 1 H 0 0 ; qtot 0 19 H 10 CHR H3 19 1 1 H 0 0 
> ; qtot 0 20 H 10 CHR H6 20 -1 1 H 0 0 ; qtot 0 21 H 11 CHR H3 21 1 1 H 0 
> 0 ; qtot 0 22 H 11 CHR H6 22 -1 1 H 0 0 ; qtot 0 23 H 12 CHR H3 23 1 1 H 
> 0 0 ; qtot 0 24 H 12 CHR H6 24 -1 1 H 0 0 ; qtot 0 25 H 13 CHR H3 25 1 1 
> H 0 0 ; qtot 0 26 H 13 CHR H6 26 -1 1 H 0 0 ; qtot 0

This is a little hard to interpret without line breaks throughout.

-Justin

> Thanks,
> Alex Marshall
> 
> 

-- 
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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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