Bug #635

position restraints output with gmxdump -sys is wrong

Added by Floris Buelens almost 10 years ago. Updated over 4 years ago.

analysis tools
Target version:
Affected version - extra info:
Affected version:


gmxdump output for position restraints is incorrect when the option -sys is used. Tested with 4.0.5 and 4.5.3. Steps to reproduce:
wget '' -O 1AKI.pdb
pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce
editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p
[add -DPOSRES]
grompp -f minim.mdp -c 1AKI_solv.gro -p -o em.tpr
gmxdump -s em.tpr > gmxdump.mdp
gmxdump -sys -s em.tpr > gmxdump_sys.mdp

now gmxdump.mdp has a healthy Position Rest. section starting like this:

Position Rest.:
nr: 2002
0 type=409 (POSRES) 0
1 type=410 (POSRES) 4
2 type=411 (POSRES) 6
3 type=412 (POSRES) 9
4 type=413 (POSRES) 12
5 type=414 (POSRES) 15

and gmxdump_sys.mdp looks like:

Position Rest.:
nr: 2002
0 type=0 (LJ_SR) 0 1
1 type=4 (LJ_SR) 2 6
2 type=3 (LJ_SR) 9 4
3 type=12 (LJ_SR) 5 15
4 type=6 (LJ_SR) 18 7
5 type=22 (LJ_SR) 8 23

The first functype=POSRES entry starts with index 409. With -sys the entries start from type 0 and the whole section is messed up.

Associated revisions

Revision ced146e9 (diff)
Added by Mark Abraham almost 8 years ago

Noting that and why gmxdump -s -sys is broken

Not worth fixing. You could pass a boolean from gmxdump
into the set_posres_params to avoid executing the
problematic line, but that would hit a lot of
other code paths that also call gmx_mtop_to_t_topology.

Refs #635

Change-Id: I308e59287dc578b95ea67c313867df3e75047fa4


#1 Updated by Floris Buelens over 9 years ago

commenting out this line:

/* Set the parameter index for idef->iparams_posre */
il->iatoms[i*2] = i;

in mtop_util.c seems to fix gmxdump -sys functionality but I would guess this has some knock-on effects...?

#2 Updated by Rossen Apostolov over 9 years ago

  • Assignee set to Berk Hess
  • Target version changed from 4.5.1 to 4.5.5

#3 Updated by Szilárd Páll about 9 years ago

  • Target version changed from 4.5.5 to 4.5.6

#4 Updated by Mark Abraham almost 8 years ago

  • Category set to analysis tools
  • Status changed from New to Feedback wanted
  • Target version changed from 4.5.6 to future

I made to note that this bug exists and comment where the code is that triggers it. But with the likelihood of massive code changes, and the low impact of the bug, it is not worth fixing.

#5 Updated by Rossen Apostolov almost 7 years ago

  • Status changed from Feedback wanted to Rejected
  • Affected version set to 4.5.3

As Mark pointed out, it's not worth fixing, thus closing the report.

#6 Updated by Mark Abraham over 4 years ago

  • Target version deleted (future)

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