[gmx-users] trjconv error

[Justin Lemkul]

On Thu, Nov 21, 2013 at 5:50 PM, Rama <ramkishna72 at gmail.com> wrote:

> Hi
>
> After MD run, lipids are broken at the boundaries. I'm trying to fix
> trajectory by following command
>
> trjconv -f a.trr -o a1.trr -s b.tpr -pbc mol
>
> then I use a1.trr file(output file from above command) to make snapshots by
> following command:
>
> trjconv -s b.tpr -f a1.trr -o c.gro -skip 5 -sep
>
> it shows some fatal error:
> Fatal error:
> Index[8271] 8272 is larger than the number of atoms in the
> trajectory file (8271). There is a mismatch in the contents
> of your -f, -s and/or -n files.
>
>
You haven't shown what group you are choosing for output in the first
invocation of trjconv, but it is fairly clear that you  are not saving all
the necessary coordinates.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
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


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