[gmx-users] PROTEIN FOLDING

[Neha Gupta]

At first, I gave,
gmx trjconv -pbc whole -s prd.tpr -f prd.xtc -o trajwhole.xtc
 I selected "system" for output

It says
Program gmx trjconv, VERSION 5.1.4
Source code file:
/cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/gmx_trjconv.c,
line: 1322

Fatal error:
Index[6376] 6377 is larger than the number of atoms in the
trajectory file (6376). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Which index number should I select for all the three commands mentioned
above?

Thanks,
Neha



On Sat, Dec 30, 2017 at 9:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/30/17 10:47 AM, Alexandr Nasedkin wrote:
>
>> gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc nojump -o trajclust.xtc -n
>> index.ndx -center
>>
>>
> Removing jumps and centering simultaneously should be considered mutually
> exclusive. One usually needs a few rounds of trjconv, e.g.
>
> gmx trjconv -pbc whole
> gmx trjconv -pbc nojump
> gmx trjconv -pbc mol -center
>
> Almost always does the trick for simple systems.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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>
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