[gmx-users] regarding rmsd calculation

[SHAHEE ISLAM]

hi,
i am doing thr rmsd calculation of protein,by using the command
gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic.tpr -f
../pbc.xtc/md-0-1.xtc -o rmsd-p1-0-1.xvg -tu ns   (this is for first 1
microsecond)
then again i have done for the next 1 micro second
gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic1.tpr -f
../pbc.xtc/md-1-2.xtc -o rmsd-p1-1-2.xvg -tu ns (i.e from 1 to 2
microsecond)
but the problem is there is no continuity between the last valu of
rmsd-p1-0-1.xvg and last value of rmsd-p1-1-1.xvg

rmsd-p1-0-1.xvg
 0.0000000    0.0049827
   0.0200000    0.1721005
   0.0400000    0.2209484
   0.0600000    0.2384352
.
.
.

999.9400635    0.8320900
 999.9600220    0.8242129
 999.9800415    0.8163539
1000.0000610    0.8269945

and the rmsd-p1-1-1.xvg
0.0000000    0.0049169
   0.0200000    0.1181309
   0.0400000    0.1274706
   0.0600000    0.1289782
.
.
.
999.9400635    0.5308270
 999.9600220    0.5303858
 999.9800415    0.5313085
1000.0000610    0.5300161
 the last value of rmsd-p1-0-1.xvg should almost equal to the first
value of rmsd-p1-1-1.xvg as it is the continuation value starting from
one microsecond. i did not understand why this is happening.
thanking you
shahee