[gmx-users] Structure averaging problem using g_rmsf

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 23 03:30:44 CET 2012

Spring buds wrote:
> Hi
> I am trying to average the structure from the last 10ns from 100ns. So I 
> used the command which is below:
> g_rmsf –f 100.xtc –s topol.tpr –b 90001 –e 100000 –ox traj_avg.pdb
> But I got below error: 
> "Program g_rmsf, VERSION 4.5.4
> Source code file: /root/Desktop/gromacs-4.5.4/src/gmxlib/trxio.c, line: 713
> Fatal error:
> Specified frame doesn't exist or file not seekable"

You're specifying a frame that doesn't exist, either 90001 or 100000.  Likely 
90001 is not an actual time in the trajectory, thus giving rise to the "not 
seekable" error.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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