Here is how to use the rms program to calculate
rms and fluctuation 
Needed file are: connectivity , coordintes of the reference structure and 
coordinates obtained during dynamics simulation .
below is a sample input

~
~  RMS TEST
~
file conn name=(wcon.mbco) unit=10 read
file rcrd name=(MBCO.MIN.CRD) unit=11 read
file rdyc name=(MBCO.DCD) bina  unit=12 read
file wrms name=(rms.data) unit=14 wovr
file wave name=(rms_ave.data) unit=15 wovr
file wflu name=(flu.data) unit=16 wovr
#crd=100 #ste=1000 step=0.002
action


#ste - number of steps in the dynamics simulation
#crd - number of steps between coordinate sets
step - time step in ps

rms.data -  result rms between dynamics structure and reference structure
rms_ave.data - result rms between dynamics structrue and average structure
flu.data - fluctuation from average struction ( (r-)^2 )   
If you only want one of them , what you need to do is remove other two lines
in the input.
For example,if you want only rms.data, the input is 
~
~  RMS TEST
~
file conn name=(wcon.mbco) unit=10 read
file rcrd name=(MBCO.MIN.CRD) unit=11 read
file rdyc name=(MBCO.DCD) bina  unit=12 read
file wrms name=(rms.data) unit=14 wovr
#crd=100 #ste=1000 step=0.002
action


below is the standard output

fluctuation> ~
fluctuation> ~ DYNAMICS TEST
fluctuation> ~
fluctuation> file conn name=(wcon.mbco) unit=10 read
fluctuation> file rcrd name=(MBCO.MIN.CRD) unit=11 read
getcrd> * title for CHARMM coordinates
getcrd> *
fluctuation> file rdyc name=(MBCO.DCD) bina  unit=12 read
fluctuation> file wrms name=(rms.data) unit=14 wovr
fluctuation> #crd=100 #ste=1000 step=0.002
fluctuation> action
  READING DYNAMICS CRD, STRUCTURE #  1
  rotation matrix 
 .9999999999927429 2.642858385206576E-06 2.744106114227484E-06
 -2.642869632723640E-06 .9999999999881071 4.098891828923495E-06
 -2.744095281424080E-06 -4.098899081242629E-06 .9999999999878348
  After overlap rms is =  .1800677569844866
  READING DYNAMICS CRD, STRUCTURE #  2
  rotation matrix 
 .9999999997731057 1.219989243025524E-05 1.746289086074909E-05
 -1.220010823773631E-05 .9999999998492188 1.235800795341013E-05
 -1.746274009178233E-05 -1.235822099971166E-05 .9999999997711643
  After overlap rms is =  .3206856287223989
  READING DYNAMICS CRD, STRUCTURE #  3
  rotation matrix 
 .9999999996325165 4.004725312505257E-06 2.681284716665732E-05
 -4.004024638479703E-06 .9999999996505422 -2.613203795784942E-05
 -2.681295180890358E-05 2.613193058893445E-05 .9999999992990935
  After overlap rms is =  .4447835002218578
  READING DYNAMICS CRD, STRUCTURE #  4
  rotation matrix 
 .9999999994612092 3.091141573821965E-05 -1.104836711908474E-05
 -3.091149265264087E-05 .9999999994980089 -6.961487758115787E-06
 1.104815192408750E-05 6.961829275893387E-06 .9999999999147361
  After overlap rms is =  .5234805210556039
  READING DYNAMICS CRD, STRUCTURE #  5
  rotation matrix 
 .9999999966409292 7.807992912594330E-05 -2.493321283645113E-05
 -7.807987782327046E-05 .9999999969496477 2.058565041526466E-06
 2.493337349297047E-05 -2.056618252384680E-06 .9999999996870484
  After overlap rms is =  .5859792965449386
  READING DYNAMICS CRD, STRUCTURE #  6
  rotation matrix 
 .9999999951942369 7.925194567436919E-05 5.771182729550141E-05
 -7.925096753584148E-05 .9999999967159779 -1.695075879757970E-05
 -5.771317048658755E-05 1.694618499797928E-05 .9999999981910089
  After overlap rms is =  .6540930897502345
  READING DYNAMICS CRD, STRUCTURE #  7
  rotation matrix 
 .999999985564983 1.070426953304924E-04 1.319541357243832E-04
 -1.070417189140322E-04 .9999999942436046 -7.406707871853801E-06
 -1.319549277988066E-04 7.392583167415887E-06 .9999999912666236
  After overlap rms is =  .7424947261572076
  READING DYNAMICS CRD, STRUCTURE #  8
  rotation matrix 
 .9999999929847465 1.180966651069081E-04 -9.147913594558659E-06
 -1.180951365161499E-04 .9999999790959805 1.669178782365706E-04
 9.167625848065242E-06 -1.669167967414957E-04 .9999999860273685
  After overlap rms is =  .8007353643772485
  READING DYNAMICS CRD, STRUCTURE #  9
  rotation matrix 
 .9999999957592453 7.789672531365662E-05 -4.912850703480894E-05
 -7.787871896783624E-05 .9999999298390524 3.664106927434027E-04
 4.915704578100505E-05 -3.664068651243663E-04 .9999999316647944
  After overlap rms is =  .8447578167717348
  READING DYNAMICS CRD, STRUCTURE #  10
  rotation matrix 
 .9999999994376918 3.231737448911736E-05 -8.955677125409290E-06
 -3.231343068263637E-05 .9999999026690097 4.400202425462557E-04
 8.969896552749739E-06 -4.400199529101490E-04 .9999999031509859
  After overlap rms is =  .8771241859329588