[gmx-users] regarding rmsd calculation

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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