On 6/4/18 8:57 AM, SHAHEE ISLAM wrote:
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 fact that your time values restarted suggests that the simulation
did not continue from the previous time, rather it restarted from zero
and you have essentially two separate simulations of 1 microsecond. What
does visual inspection of the trajectory tell you?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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