[gmx-users] Error in system_inflate.gro coordinates does not match

[Dallas Warren]

That is not possible.

Turn on the periodic image in the direction in which it appears to you that the protein is "out".  Even turn on all six, play with them all, on and off in different combinations, to see what it shows.  The PBC is an important concept that you need to get your head around.

If you still think it is "out", then you need to provide us with images showing what you think it going on, then we can explain what you are actually seeing.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 


> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> RINU KHATTRI
> Sent: Wednesday, 16 July 2014 3:41 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error in system_inflate.gro coordinates does
> not match
> 
> hello every one
> i saw it in vmd representation ->periodic but still protein is out
> 
> 
> On Wed, Jul 16, 2014 at 11:01 AM, Dallas Warren
> <Dallas.Warren at monash.edu>
> wrote:
> 
> >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Cond
> itions
> >
> > Switch on periodic image in VMD and you will that it is not a problem
> at
> > all.
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Drug Delivery, Disposition and Dynamics
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3052
> > dallas.warren at monash.edu
> > +61 3 9903 9304
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to
> resemble a
> > nail.
> >
> >
> > > -----Original Message-----
> > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> > > [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On
> Behalf Of
> > > RINU KHATTRI
> > > Sent: Wednesday, 16 July 2014 3:24 PM
> > > To: gmx-users at gromacs.org
> > > Subject: Re: [gmx-users] Error in system_inflate.gro coordinates
> does
> > > not match
> > >
> > > hello gromacs users
> > > i saw  in vmd system.gro its little bit ok very small fragment of
> > > protein
> > > is out but in shrinkage.gro file box and protein is separated
> > >
> > > ; Include Position restraint file
> > > #ifdef POSRES
> > > #include "posre.itp"
> > > #endif
> > > ; Strong position restraints for InflateGRO
> > > #ifdef STRONG_POSRES
> > > #include "strong_posre.itp"
> > > #endif
> > >
> > > ; Include ligand topology
> > > #include "drag.itp"
> > >
> > > ; Include POPC chain topology
> > > #include "popc.itp"
> > >
> > > ; Include water topology
> > > #include "gromos53a6_lipid.ff/spc.itp"
> > >   my topology file
> > > kindly help
> > > thanks in advance
> > >
> > >
> > > On Wed, Jul 16, 2014 at 10:20 AM, RINU KHATTRI
> > > <nickname.mittu at gmail.com>
> > > wrote:
> > >
> > > > hello every one
> > > > i am working on complex with popc membrane after visualization of
> > > minimize
> > > > structure (after solvation and addition of ions 14 cl-) in VMD i
> saw
> > > > protein is moving out em.gro from the lipid membrane i dont know
> how
> > > to
> > > > resolve it
> > > >
> > > > help
> > > >
> > > >
> > > > On Tue, Jul 15, 2014 at 3:42 PM, RINU KHATTRI
> > > <nickname.mittu at gmail.com>
> > > > wrote:
> > > >
> > > >> hello everyone
> > > >> now i got the minimize structure after addition of water and
> ions
> > > (14 cl-)
> > > >> i have been select  the
> > > >>
> > > >> genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname
> NA -
> > > nname CL -nn 14
> > > >>
> > > >> 13 th option  sol  in out put
> > > >>
> > > >> how can i analyze  my structure means is it ok or not because
> next
> > > step is equilibration
> > > >>
> > > >> kindly help
> > > >>
> > > >>
> > > >>
> > > >> On Sat, Jul 12, 2014 at 2:48 AM, Justin Lemkul <jalemkul at vt.edu>
> > > wrote:
> > > >>
> > > >>>
> > > >>>
> > > >>> On 7/11/14, 3:18 AM, RINU KHATTRI wrote:
> > > >>>
> > > >>>> hello
> > > >>>> i am following the lysozyme tutorial
> > > >>>>
> > > >>>> editconf -f system_shrink20.gro -o newbox.gro -bt dodecahedron
> -d
> > > 1.0
> > > >>>>
> > > >>>
> > > >>> Don't alter the box like this; it's totally nonsensical.
> > > >>>
> > > >>>
> > > >>>    solvate -cp newbox.gro -cs spc216.gro -p topol.top -o
> solv.gro
> > > >>>>
> > > >>>>   but after running second command i got error  solvate
> command
> > > not
> > > >>>> found
> > > >>>>
> > > >>>> gmx solvate is also not working
> > > >>>>
> > > >>>>
> > > >>> The tutorial corresponds to version 5.0; if you're using an
> older
> > > >>> version, the command is called "genbox."
> > > >>>
> > > >>>
> > > >>> -Justin
> > > >>>
> > > >>> --
> > > >>> ==================================================
> > > >>>
> > > >>> Justin A. Lemkul, Ph.D.
> > > >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > > >>>
> > > >>> Department of Pharmaceutical Sciences
> > > >>> School of Pharmacy
> > > >>> Health Sciences Facility II, Room 601
> > > >>> University of Maryland, Baltimore
> > > >>> 20 Penn St.
> > > >>> Baltimore, MD 21201
> > > >>>
> > > >>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > >>> http://mackerell.umaryland.edu/~jalemkul
> > > >>>
> > > >>> ==================================================
> > > >>> --
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> > > >>
> > > >>
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