[gmx-users] g_rmsf => average over # of time frames ???

[Mark Abraham]

If the reference structure from which the fluctuations are measured is taken from the -s file (check the documentation or code), then a non-equilibrium trajectory could well have this property w.r.t. a crystal structure.

Mark

----- Original Message -----
From: Chih-Ying Lin <chihying2008 at gmail.com>
Date: Tuesday, October 26, 2010 15:55
Subject: [gmx-users] g_rmsf => average over # of time frames ???
To: gmx-users at gromacs.org

> 
> 
> Hi > 
> From source code => gmx_rmsf.c > "g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard ",
  >     "deviation) of atomic positions ",
 > 
>     if (devfn) {
 >       /* Calculate RMS Deviation */
 >       for(i=0;(i<isize);i++) {
 > 	aid = index[i];
 > 	for(d=0;(d<DIM);d++) {
  > 	  rmsd_x[i][d] += sqr(x[aid][d]-xref[aid][d]);
 > 	}
 >       }
 >     } 
 >     count += 1.0;
 > 
> rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;
 > 

> 

> Therefore, g_rmsf is the average of structure deviation over the time frames.
 > 

> However, I issued the commands  ( C-alpha is selected )
 > g_rmsf -f abc.xtc -b 0 -e 100 -s abc-crystal.tpr -o RMSF-abc-0th-100th.xvg
 > g_rmsf -f abc.xtc -b 100 -e 200 -s abc-crystal.tpr -o RMSF-abc-100th-200th.xvg
> g_rmsf -f abc.xtc -b 200 -e 300 -s abc-crystal.tpr -o RMSF-abc-200th-300th.xvg
 > g_rmsf -f abc.xtc -b 300 -e 400 -s abc-crystal.tpr -o RMSF-abc-300th-400th.xvg
 > g_rmsf -f abc.xtc -b 400 -e 500 -s abc-crystal.tpr -o RMSF-abc-400th-500th.xvg
> g_rmsf -f abc.xtc -b 500 -e 600 -s abc-crystal.tpr -o RMSF-abc-500th-600th.xvg
 > g_rmsf -f abc.xtc -b 600 -e 700 -s abc-crystal.tpr -o RMSF-abc-600th-700th.xvg
 > g_rmsf -f abc.xtc -b 700 -e 800 -s abc-crystal.tpr -o RMSF-abc-700th-800th.xvg
> g_rmsf -f abc.xtc -b 800 -e 900 -s abc-crystal.tpr -o RMSF-abc-800th-900th.xvg
 > g_rmsf -f abc.xtc -b 900 -e 1000 -s abc-crystal.tpr -o RMSF-abc-900th-1000th.xvg
 > 

> 

 > Also, (  C-alpha is selected )
> g_rmsf -f abc.xtc -b 0 -e 1000 -s abc-crystal.tpr -o RMSF-abc-0th-1000th.xvg
 > 

> 
 
> 

> Then I ploted, 
 > RMSF-abc-0th-100th.xvg
> RMSF-abc-100th-200th.xvg
 > RMSF-abc-200th-300th.xvg
> RMSF-abc-300th-400th.xvg
 > RMSF-abc-400th-500th.xvg
> RMSF-abc-500th-600th.xvg
 > RMSF-abc-600th-700th.xvg
> RMSF-abc-700th-800th.xvg
 > RMSF-abc-800th-900th.xvg
> RMSF-abc-900th-1000th.xvg
 > 

> 
 
> Also, I ploted
 > RMSF-abc-0th-1000th.xvg
> 

 > 

> 
 
> The PLOT RMSF-abc-0th-1000th.xvg has all RMSF-Values much higher than those from RMSF-abc-0th-100th.xvg / RMSF-abc-100th-200th.xvg / RMSF-abc-200th-300th.xvg / ......   / RMSF-abc-900th-1000th.xvg.......
 > 

> 
 
> It does not make sense... I supposed.....
 > Did I misunderstand something ?
> 
 
> 

> 
 
> THank you
> Lin
 > 

> 
 
> 

> 
 
> 

> 
 
> 

 > -- 
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