Hi again! Anyone with any suggestions? I am totally stuck with this... 2016-10-03 12:15 GMT+03:00 Sophia Kuriakidi <skyriak...@gmail.com>:
> 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? 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