Hi, Did you start with http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-features.html#running-a-membrane-protein-embedding-simulation?
Mark On Sun, 2 Oct 2016 17:13 Sophia Kuriakidi <skyriak...@gmail.com> wrote: > Hi again to all of you! > I am trying to run at last this membrane simulation. I am trying to use the > -membed option but I can't figure out how to. Can anyone provide me with an > example input line? e.g. gmx mdrun -membed -input file -n index.ndx -p > topol.top -o output file etc ? And also, can anyone provide with an example > embed.dat? Thanks a lot in advance! > > 2016-09-22 10:38 GMT+03:00 Sophia Kuriakidi <skyriak...@gmail.com>: > > > Thank you so much Tom, I will try that! > > > > 2016-09-21 21:11 GMT+03:00 Thomas Piggot <t.pig...@soton.ac.uk>: > > > >> g_membed is now part of mdrun, so you would need to use mdrun with the > >> -membed option. From mdrun -h: > >> > >> /"The option -membed does what used to be g_membed, i.e. embed a protein > >> into a// > >> //membrane. This module requires a number of settings that are provided > >> in a// > >> //data file that is the argument of this option. For more details in > >> membrane// > >> //embedding, see the documentation in the user guide. The options -mn > and > >> -mp// > >> //are used to provide the index and topology files used for the > >> embedding."/ > >> > >> Cheers > >> > >> Tom > >> > >> > >> On 21/09/16 18:36, Sophia Kuriakidi wrote: > >> > >>> Thank you for your responses! > >>> > >>> Sotirios:"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." > >>> I also have grouped the ligand with the protein (but not any waters) > and > >>> I > >>> included the index in the mdp file. > >>> > >>> Thomas:"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)." > >>> > >>> It seems that this is the case because I am using 5.1.2. How could I > >>> resolve this problem? How coould I use g_membed in 5.1.2? Or how I > could > >>> alternatively insert my protein into a membrane bilayer? > >>> > >>> Thanks again! > >>> > >>> > >>> > >>> 2016-09-14 13:47 GMT+03:00 Thomas Piggot <t.pig...@soton.ac.uk>: > >>> > >>> 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! > >>>>> -- > >>>>> Gromacs Users mailing list > >>>>> > >>>>> * Please search the archive at http://www.gromacs.org/Support > >>>>> /Mailing_Lists/GMX-Users_List before posting! > >>>>> > >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>> > >>>>> * For (un)subscribe requests visit > >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > >>>>> send a mail to gmx-users-requ...@gromacs.org. > >>>>> > >>>>> -- > >>>> Dr Thomas Piggot > >>>> Visiting Fellow > >>>> University of Southampton, UK. > >>>> > >>>> > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at http://www.gromacs.org/Support > >>>> /Mailing_Lists/GMX-Users_List before posting! > >>>> > >>>> * Can't post? 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