[gmx-users] Slab Ewald test

Alex Marshall amarsh59 at uwo.ca
Wed Jul 13 21:46:38 CEST 2011


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
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?

.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
Thanks,
Alex Marshall
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