Hi Mark, Yes I started with the tutorial you mentioned. From which I understood I need some kind of embed.dat file and that my .mdp file has to have this part: integrator = md energygrps = Protein_Lig (since I have a ligand and I have grouped it with the protein using an index file) freezegrps = Protein_Lig freezedim = Y Y Y energygrp_excl = Protein_Lig Protein_Lig
I copied this to the embed file: xyinit (0.5) Resize factor for the protein in the xy dimension before starting embedding. - xyend 1.0 zinit 1.0 - zend 1.0 - nxy 1000 - nz 0 - rad 0.22 - pieces 1 - asymmetry no - ndiff 0 - maxwarn 0 - - Is that correct? And what is the appropriate command in order to actually run the simulation? - I am sorry if I am asking something obvious, I am completely new to gromacs! Thanks! 2016-10-02 19:28 GMT+03:00 Mark Abraham <mark.j.abra...@gmail.com>: > 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? 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? 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. > > >> > > > > > > > > -- > > 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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