[gmx-users] Problems with Ion

[Fábio Filippi Matioli]

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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