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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
