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