Re: [gmx-users] g_membed failure

2016-10-17 Thread Tsjerk Wassenaar
> >>>> 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 shou

Re: [gmx-users] g_membed failure

2016-10-17 Thread Sophia Kuriakidi
>>>> 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 tr

Re: [gmx-users] g_membed failure

2016-10-03 Thread Sophia Kuriakidi
t;> 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.

Re: [gmx-users] g_membed failure

2016-10-02 Thread Mark Abraham
27;t be possible). > >>>> > >>>> Cheers > >>>> > >>>> Tom > >>>> > >>>> > >>>> On 14/09/16 08:40, Sotirios Dionysios I. Papadatos wrote: > >>>> > >>>> Hi, run

Re: [gmx-users] g_membed failure

2016-10-02 Thread Sophia Kuriakidi
t;>> >>>> 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

Re: [gmx-users] g_membed failure

2016-09-22 Thread Sophia Kuriakidi
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

Re: [gmx-users] g_membed failure

2016-09-21 Thread Thomas Piggot
oun...@maillist.sys.kth.se < gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sophia Kuriakidi 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 embe

Re: [gmx-users] g_membed failure

2016-09-21 Thread Sophia Kuriakidi
n 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-use

Re: [gmx-users] g_membed failure

2016-09-14 Thread Thomas Piggot
for it to work. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Sophia Kuriakidi 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

Re: [gmx-users] g_membed failure

2016-09-14 Thread Sotirios Dionysios I. Papadatos
_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://ww

[gmx-users] g_membed failure

2016-09-13 Thread Sophia Kuriakidi
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 * I am creating an input

[gmx-users] g_membed failure

2016-09-13 Thread Sophia Kuriakidi
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 * I am creating an input