Thank you for your reply. I see box in the .g87 file. And
if I try choice 3, I get the following and end up segementation fault
again. <br><br>
------------------------------------------------------------------------------------------------------------------<br>
g_gyrate -f nmwt.g87 -s nmwt.tpr -n index.ndx<br>
<br>
<br>
:-) G R O M A C S (-:<br>
<br>
GROningen Mixture of Alchemy and Childrens' Stories<br>
<br>
:-) VERSION 3.3 (-:<br>
<br>
<br>
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
Copyright (c) 2001-2004, The GROMACS development team,<br>
check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br>
<br>
This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br>
as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.<br>
<br>
:-) g_gyrate (-:<br>
<br>
Option Filename Type Description<br>
------------------------------------------------------------<br>
-f nmwt.g87
Input Generic trajectory: xtc
trr trj gro g96 pdb<br>
-s nmwt.tpr
Input Structure+mass(db): tpr
tpb tpa gro g96 pdb<br>
xml<br>
-n index.ndx Input, Opt! Index file<br>
-o gyrate.xvg Output xvgr/xmgr file<br>
-acf moi-acf.xvg Output, Opt. xvgr/xmgr file<br>
<br>
Option Type Value Description<br>
------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>
-[no]X
bool no Use dialog box GUI to edit
command line options<br>
-nice int 19 Set the nicelevel<br>
-b
time 0 First frame (ps) to read
from trajectory<br>
-e
time 0 Last frame (ps) to read from
trajectory<br>
-dt
time 0 Only use frame when t MOD dt
= first time (ps)<br>
-[no]w bool no View output xvg, xpm, eps and pdb files<br>
-[no]xvgr bool yes Add specific codes (legends etc.) in the output<br>
xvg files for the xmgrace program<br>
-nmol
int 1 The number of molecules to
analyze<br>
-[no]q
bool no Use absolute value of the charge
of an atom as<br>
weighting factor instead of mass<br>
-[no]p
bool no Calculate the radii of gyration
about the<br>
principal axes.<br>
-[no]moi bool
no Calculate the moments of inertia (defined by the<br>
principal axes).<br>
-acflen
int -1 Length of the ACF, default is half
the number of<br>
frames<br>
-[no]normalize bool yes Normalize ACF<br>
-P
enum 0 Order of Legendre polynomial
for ACF (0 indicates<br>
none): 0, 1, 2 or 3<br>
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,<br>
exp5, exp7 or exp9<br>
-ncskip
int 0 Skip N points in the output
file of correlation<br>
functions<br>
-beginfit real 0 Time where to begin the exponential fit of the<br>
correlation function<br>
-endfit real -1 Time where to end the exponential fit of the<br>
correlation function, -1 is till the end<br>
<br>
Reading file nmwt.tpr, VERSION 3.3 (single precision)<br>
Reading file nmwt.tpr, VERSION 3.3 (single precision)<br>
Group 0 ( System) has 17351 elements<br>
Group 1 ( Protein) has 732 elements<br>
Group 2 ( Protein-H) has 366 elements<br>
Group 3 ( C-alpha) has 52 elements<br>
Group 4 ( Backbone) has 156 elements<br>
Group 5 ( MainChain) has 209 elements<br>
Group 6 (MainChain+Cb) has 250 elements<br>
Group 7 ( MainChain+H) has 260 elements<br>
Group 8 ( SideChain) has 472 elements<br>
Group 9 ( SideChain-H) has 157 elements<br>
Group 10 ( Prot-Masses) has 732 elements<br>
Group 11 ( Non-Protein) has 16619 elements<br>
Group 12 ( Cl-) has 5 elements<br>
Group 13 ( WAT) has 16614 elements<br>
Group 14 ( Other) has 16619 elements<br>
Select a group: 1<br>
Selected 1: 'Protein'<br>
<br>
<br>
Select File Format<br>
---------------------------<br>
1. XYZ File<br>
2. XYZ File with Box<br>
3. Gromos-87 Ascii Trajectory<br>
4. Gromos-87 Ascii Trajectory with Box<br>
<br>
Choice: 3<br>
<br>
GROMOS! OH DEAR...<br>
<br>
Number of atoms ? 17351<br>
Time between timeframes ? 1<br>
Box X Y Z ? 6.40310 5.96850 4.57077<br>
<br>
<br>
Reading frame 790 time 791.000 error reading statusfile: x[800][0]<br>
<br>
Back Off! I just backed up gyrate.xvg to ./#gyrate.xvg.6#<br>
Segmentation fault<br>
------------------------------------------------------------------------------------------------------------<br>
<br>
Sincerely<br>
Lydia<br>
<br><br>