Hi,
In more recent versions of GROMACS (4.6.x and above IIRC), the g_membed
feature is only available using mdrun (see mdrun -h) and so the g_membed
command should either no longer work at all or print you a note to tell
you to use mdrun (depending upon version).
My guess is that you probably also have an older version of the g_membed
program installed on your system and as you are trying to use a more
recent tpr (from version 5.1.2), this might be what is causing the
segmentation fault. That said, if I try a tpr from GROMACS 5.0.6 with
g_membed 4.5.7 it does give me a warning about a mismatch of versions so
I could be wrong (but what you say you are doing shouldn't be possible).
Cheers
Tom
On 14/09/16 08:40, Sotirios Dionysios I. Papadatos wrote:
Hi, run some diagnostics, don't use the -xyinit etc
Try the basics gmx g_membed -f -p ... etc
Also the way this worked for me was to use an index file. I made an index of
the prot + lig + crystallographic waters and I used it in both grompp and
g_membed. In the latter I just used the
group and then selected the POPC. You must also include the group's name in the
mdp in order for it to work.
________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sophia Kuriakidi
<skyriak...@gmail.com>
Sent: Tuesday, September 13, 2016 9:18:12 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] g_membed failure
Hi all,
I am trying to use g_membed in order to embed my protein in a lipid bilayer
(I am using dppc). I am using the tutorial of Appendix A of this paper:
*http://wwwuser.gwdg.de/~ggroenh/submitted/Membed_rev.pdf
<http://wwwuser.gwdg.de/~ggroenh/submitted/Membed_rev.pdf>*
I am creating an input.tpr using this command:
grompp -f sample.mdp -c merged.gro -p merged.top -o input.tpr
and it works fine. Then when I am trying to use g_membed by typping this:
g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
or this
g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
-zinit 1.1 -zend 1.0 -nz 100
I just get the g_membed manual printed out...
$ g_membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
Option Filename Type Description
------------------------------------------------------------
-f input.tpr Input Run input file: tpr tpb tpa
-n index.ndx Input, Opt. Index file
-p merged.top In/Out, Opt! Topology file
-o traj.trr Output Full precision trajectory: trr trj cpt
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr
format)
-cpi state.cpt Input, Opt. Checkpoint file
-cpo state.cpt Output, Opt. Checkpoint file
-c membedded.gro Output Structure file: gro g96 pdb etc.
-e ener.edr Output Energy file
-g md.log Output Log file
-ei sam.edi Input, Opt. ED sampling input
-rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-table table.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-tableb table.xvg Input, Opt. xvgr/xmgr file
-dhdl dhdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-tableb table.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-tpid tpidist.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo sam.edo Output, Opt. ED sampling output
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-px pullx.xvg Output, Opt. xvgr/xmgr file
-pf pullf.xvg Output, Opt. xvgr/xmgr file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-xyinit real 0.1 Resize factor for the protein in the xy
dimension
before starting embedding
-xyend real 1 Final resize factor in the xy dimension
-zinit real 1 Resize factor for the protein in the z dimension
before starting embedding
-zend real 1 Final resize faction in the z dimension
-nxy int 1000 Number of iteration for the xy dimension
-nz int 0 Number of iterations for the z dimension
-rad real 0.22 Probe radius to check for overlap between the
group to embed and the membrane
-pieces int 1 Perform piecewise resize. Select parts of the
group to insert and resize these with respect to
their own geometrical center.
-[no]asymmetry bool no Allow asymmetric insertion, i.e. the number of
lipids removed from the upper and lower leaflet
will not be checked.
-ndiff int 0 Number of lipids that will additionally be
removed from the lower (negative number) or
upper
(positive number) membrane leaflet.
-maxwarn int 0 Maximum number of warning allowed
-[no]compact bool yes Write a compact log file
-[no]v bool no Be loud and noisy
Back Off! I just backed up md.log to ./#md.log.2#
Reading file input.tpr, VERSION 5.1.2 (single precision*)*
*Segmentation fault (core dumped)*
Along with this highlighted message...
I can't figure out what's wrong, please I could use some help!
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--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.
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