[gmx-users] trjconv : error

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello,
> I am trying to calculate spatial distribution function (SDF) for my system.
> 
>  1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n
> test.ndx
> 2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n test.ndx
> 
> I am getting the following error for step 2.
> 
> Fatal error: Index[2385] 2410 is larger than the number of atoms in the
> trajectory file (2409).
> 
> How can I solve this problem?
> Duirng my simulation I didn't specify xtc_grps  this option in md file.
> 

Then it looks like you must have saved only a subset of your system during step 
1 or some other post-processing step.  Either save the whole system, or use 
tpbconv to generate a .tpr file that contains only the relevant subset of atoms.

-Justin

> 
> 
> Thanks
> 
> Nilesh
> 
> 
> 
> 
> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================