[gmx-users] trjconv : error

Nilesh Dhumal ndhumal at andrew.cmu.edu
Tue May 11 23:18:30 CEST 2010

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
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.



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