[gmx-users] Empty output files from gmx helix?

[yunshi11 .]

Hi everyone,

I have a 21-mer peptide A for helix analysis using gmx helix in GROMACS 5.

When I select residues 3-19 when executing gmx helix, everything looks
fine. But when I select another set of residues, e.g. 8-19, the output
len-ahx.xvg file ends after:

# This file was created Thu Jun  9 12:01:28 2016
# Created by:
# GROMACS:      gmx helix, VERSION 5.0.4
# Executable:   /usr/local/gromacs/bin/gmx
# Library dir:  /usr/local/gromacs/share/gromacs/top
# Command line:
#   gmx helix -s r1_60.5.tpr -n a4.ndx -f 120fit.xtc
# gmx is part of G R O M A C S:
#
# Gnomes, ROck Monsters And Chili Sauce
#
@    title "Length of the Helix"
@    xaxis  label "Time (ps)"
@    yaxis  label "Length (nm)"
@TYPE xy



While the helicity.xvg file shows:

# This file was created Thu Jun  9 12:01:28 2016
# Created by:
# GROMACS:      gmx helix, VERSION 5.0.4
# Executable:   /usr/local/gromacs/bin/gmx
# Library dir:  /usr/local/gromacs/share/gromacs/top
# Command line:
#   gmx helix -s r1_60.5.tpr -n a4.ndx -f 120fit.xtc
# gmx is part of G R O M A C S:
#
# Giant Rising Ordinary Mutants for A Clerical Setup
#
@    title "Helicity per Residue"
@    xaxis  label "Residue"
@    yaxis  label "% of time"
@TYPE xy
         1           0
         2           0
         3           0
         4           0
         5           0
         6           0
         7           0
         8           0
         9           0
        10           0


And there are many empty files such as hb3.out.

Out of curiosity, I tried selecting residues 7-19 and 6-19, respectively.
The former gives me similar empty files/lines, while the latter looks
normal again. Residue 7 is ALA.


I also tried a similar 21-mer peptide B (only residues 13 and 17 are
different, they are ASN and ARG in peptide B instead of LYS and LYS in
peptide A), and selecting residues 8-19 gives normal output files.

This looks strange.