[gmx-users] Problems with Ion

[Fábio Filippi Matioli]

I basically do what the guide indicates...
I Run this command (pasted down) to generate the pdb with the ion on correct place and no jumps on box, but the output its different when compared with the after.gro generated after de MD on mdrun command

Command:

trjconv -pbc nojump -f full2.trr -s full.tpr -o after_full_2.pdb -b 50000 -e 50000


I putted this timed after -b and -e because I would like only the pdb with the last state of the MD, equal the after.gro

Best regards


________________
Fábio Filippi MatioliMestrando 
Departamento de Física e BiofísicaInstituto de BiociênciasUNESP - Campus de BotucatuCel (19) 9.9291.6738

> From: fabiofima at hotmail.com
> To: gmx-users at gromacs.org
> Date: Thu, 20 Nov 2014 17:30:38 -0200
> Subject: Re: [gmx-users] Problems with Ion
> 
> The trjconv have the output option .gro ???
> 
> ________________
> Fábio Filippi MatioliMestrando 
> Departamento de Física e BiofísicaInstituto de BiociênciasUNESP - Campus de BotucatuCel (19) 9.9291.6738
> 
> > Date: Wed, 19 Nov 2014 20:06:57 -0500
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Problems with Ion
> > 
> > 
> > 
> > On 11/19/14 4:30 PM, Fábio Filippi Matioli wrote:
> > > Hello, I have a new problem today with gromacs.
> > >
> > > After the mdrun,
> > > the gromcas generate a after.gro, that its the protein after the MD. But
> > >   on this file the CA ions its in different positions when compared with
> > > the movie generated on VMD using the after and the .trr, fixed the jump
> > > box using the trjconv.
> > > I would like to generate a pdb with the last frame of the MD's movie
> > >
> > > Can you help me please?
> > >
> > 
> > Invoking trjconv with complex systems is a multi-step process.  Start with the 
> > advice here:
> > 
> > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
> > 
> > -Justin
> > 
> > -- 
> > ==================================================
> > 
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > 
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > 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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