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

[Chih-Ying Lin]

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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