Project

General

Profile

Bug #236

g_nmtraj_d fails during normal mode analysis

Added by blair empty about 12 years ago. Updated almost 12 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

g_nmtraj_d v fws_nma.trr -s fws_em.tpr -o ensemble.pdb
:
) G R O M A C S (-:

Gromacs Runs On Most of All Computer Systems
:-)  VERSION 4.0  (-:

...edited for brevity... Blair

:-)  g_nmtraj_d (double precision)  (-:

Option Filename Type Description
------------------------------------------------------------
-s fws_em.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb
-v fws_nma.trr Input Full precision trajectory: trr trj cpt
-o ensemble.pdb Output Trajectory: xtc trr trj gro g96 pdb

Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-eignr string 7 String of eigenvectors to use (first is 1)
-phases string 0.0 String of phases (default is 0.0)
-temp real 300 Temperature in Kelvin
-amplitude real 0.25 Amplitude for modes with eigenvalue<=0
-nframes int 30 Number of frames to generate

trn version: GMX_trn_file (double precision)
Read mass weighted average/minimum structure with 3135 atoms from fws_nma.trr
Read 50 eigenvectors (for 3135 atoms)

Reading file fws_em.tpr, VERSION 4.0 (double precision)
Reading file fws_em.tpr, VERSION 4.0 (double precision)
ftp2fn: No filetype .???

-------------------------------------------------------
Program g_nmtraj_d, VERSION 4.0
Source code file: trxio.c, line: 243

Fatal error:
Sorry, write_trxframe_indexed can not write tpa
-------------------------------------------------------

job_files.zip (3.69 MB) job_files.zip These are the two input files which created the error (zipped). blair empty, 10/20/2008 03:33 PM

History

#1 Updated by blair empty about 12 years ago

Created an attachment (id=305)
These are the two input files which created the error (zipped).

#2 Updated by Erik Lindahl almost 12 years ago

Fixed, together with an amplitude settings bug.

Also available in: Atom PDF