[gmx-users] Re: g_rms: Too many iterations in routine JACOBI

[minnale]

Thnaks for your help Tsjerk.
One more thing I didnt understand is, if use all same commands except choosing options in make_ndx file like " 1 | r 50-80 " generated rmsd.xvg without issuing error, but if i use below mentioned commnands showing error, which way is correct? 
Thanks for your appreciation

  
>Hi JS RED,

>This usually indicates that you have a mismatch between your reference
>structure and your trajectory, which is logical as you extracted a
>specific set of coordinates from the trajectory, but used an original
>(complete) gro file.

>Hope it helps,

Tsjerk

On Thu, May 8, 2008 at 9:18 AM, minnale <minnale_gnos at rediffmail.com> wrote:
>
>
>
>  Hi all,
>  1)I made make_ndx file for my protein because i want to plot rmsd for
> specific residues in protein, so I have givenlike this 1 & r 50-80
>
>  2)Then I have used trjcat -f 1ns.xtc 2ns.xtc 3ns.xtc -n r_50_80.ndx
> -settime -o trjout , here I selected
>  Protein_&_r_50-80
>  this command ran without error,
>
>  3)After,
>  g_rms -f trjout.xtc -pbc -s em_inti.gro -pbc -o rms_3ns
>  Select group for least squares fit - 3 c-alpha
>  Select group for RMSD calculation - 3  c-alpha
>  it showed following error
>
>  Program g_rms, VERSION 3.3.1
>  Source code file: nrjac.c, line: 129
>
>  Fatal error:
>  Error: Too many iterations in routine JACOBI
>  I have searched in gmx archives regarding this problem , I found that
> mismatch between trjactory and reference structure file, but in my case both
> are matched atoms
>
>  Is there any mistake in either selecting options of making index file or I
> have given wrong option while using g_rms
>
>  Pls suggest me
>  Thanks in advance.
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