[gmx-users] g_rmsf calculation

Moutusi Manna mou2c_21 at yahoo.co.in
Fri Nov 6 12:49:16 CET 2009

Dear all,

           how can i calculate the root-mean-square fluctuation (RMSF)(last 5ns) of a group of atoms relative to their equilibrium position?

           the command i have used  is 

g_rmsf -f mer.xtc -s md_1ns.tpr -n group.ndx -o rmsf.xvg -nice 4 -b 35000 -e 36000 

where, md_1ns.tpr is the starting tpr for the production run.

Is this one correct? if not please suggest me the command for rmsf calculation after fitting to a referencee frame?

Again the output file is like.........(with 10 atoms in a group)


# GRowing Old MAkes el Chrono Sweat


@    title "RMS fluctuation"

@    xaxis  label "Atom"

@    yaxis  label "(nm)"

@TYPE xy

    1   0.0993

    2   0.0679

    3   0.0468

    4   0.1339

    5   0.0680

    6   0.0675

    7   0.0141

    8   0.1053

    9   0.1004

   10   0.0966


Can i get a single value for the whole group, except the rmsf values for each atoms in the group?

with regards,

Moutusi Manna

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