<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br>Hi gromacs users.<br><br>I need help with the old data generated by gromacs. It is about a year older.<br>I used the command and the output is:<br>syed@linux-g1cj:~/Desktop/283> g_energy -f md283.edr -o 283te.xvg<br> :-) G R O M A C S (-:<br><br> Good gRace! Old Maple Actually Chews Slate<br><br> :-) VERSION 3.0.5 (-:<br><br> Copyright (c) 1991-2001,
University of Groningen, The Netherlands<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_energy (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br> -f
md283.edr Input Generic energy: edr ene<br> -f2 ener.edr Input, Opt. Generic energy: edr ene<br> -s topol.tpr Input, Opt. Generic run input: tpr tpb tpa<br> -o 283te.xvg Output xvgr/xmgr file<br>-viol violaver.xvg Output, Opt. xvgr/xmgr file<br>-pairs pairs.xvg Output, Opt. xvgr/xmgr file<br>-corr enecorr.xvg Output, Opt. xvgr/xmgr file<br>-vis visco.xvg Output, Opt. xvgr/xmgr file<br>-ravg runavgdf.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 -1 First frame (ps) to read from trajectory<br> -e time -1 Last frame (ps) to read from trajectory<br> -[no]w bool no View output xvg, xpm, eps and pdb files<br> -[no]fee bool no Do a
free energy estimate<br> -fetemp real 300 Reference temperature for free energy calculation<br> -zero real 0 Subtract a zero-point energy<br> -[no]sum bool no Sum the energy terms selected rather than display<br> them all<br> -[no]dp bool no Print energies in high precision<br> -[no]mutot bool no Compute the total dipole moment from the components<br> -skip int 0 Skip number of frames between
data points<br> -[no]aver bool no Print also the X1,t and sigma1,t, only if only 1<br> energy is requested<br> -nmol int 1 Number of molecules in your sample: the energies<br> are divided by this number<br> -ndf int 3 Number of degrees of freedom per
molecule.<br> Necessary for calculating the heat capacity<br> -[no]fluc bool no Calculate autocorrelation of energy fluctuations<br> rather than energy itself<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 or vac<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>Opened md283.edr as single precision energy file<br>Select the terms you want from the following list<br>End your selection with 0<br> 1= Angle 2= Proper Dih. 3=Ryckaert-Bell. 4= LJ-14<br> 5= Coulomb-14
6= LJ (SR) 7= LJ (LR) 8= Coulomb (SR)<br> 9= Coul. recip. 10=Position Rest. 11= Potential 12= Kinetic En.<br> 13= Total Energy 14= Temperature 15=Pressure (bar) 16= Box-X<br> 17= Box-Y 18= Box-Z 19= Volume 20= Density (SI)<br> 21= pV 22= Vir-XX 23= Vir-XY 24= Vir-XZ<br>
25= Vir-YX 26= Vir-YY 27= Vir-YZ 28= Vir-ZX<br> 29= Vir-ZY 30= Vir-ZZ 31= Pres-XX (bar) 32= Pres-XY (bar)<br> 33= Pres-XZ (bar) 34= Pres-YX (bar) 35= Pres-YY (bar) 36= Pres-YZ (bar)<br> 37= Pres-ZX (bar) 38= Pres-ZY (bar) 39= Pres-ZZ (bar) 40= #Surf*SurfTen<br> 41= Pcoupl-Mu-XX 42= Pcoupl-Mu-YY 43= Pcoupl-Mu-ZZ 44= Mu-X<br> 45= Mu-Y 46= Mu-Z 47= T-Protein 48=
T-Non-Protein<br> 49= Lamb-Protein 50=Lamb-Non-Protein<br>13<br>0<br>Fatal error: Could not open 283te.xvg<br>syed@linux-g1cj:~/Desktop/283> <br><br>your help is necessary for my success.<br><br> <div><strong><font color="#007f40">Regards<br>LAL BADSHAH <br></font></strong></div><strong><font color="#007f40"></font></strong></td></tr></table><br>
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