[gmx-users] Problems with Ion

[Justin Lemkul]

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

-- 
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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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