[gmx-users] regarding rmsd calculation

[SHAHEE ISLAM]

hello sir,
there are two proteins in a water box system.i am doing martini
protein cg simulation and following this tutorial
http://cgmartini.nl/index.php/tutorials-general-introduction/protein
at the 7 no step i have done
 grompp -f dynamic.mdp -c equilibration.gro -p system.top -o dynamic.tpr
 mdrun -deffnm dynamic -v
and run for 1 micro second.from this i have got
dynamic.xtc,dynamic.gro,dynamic.edr,dynamic.log,dynamic.cpt,dynamic_prev.cpt
and to go for continuting of the simulation from 1 to 2 microsecond i have done
 grompp -f dynamic.mdp -c dynamic.gro -p system.top -o dynamic1.tpr
 mdrun -deffnm dynamic1 -v
from the visual inspection there is not that much of difference
between the two .xtc file.
did i have done any wrong for the continuity of the simulation.
thanking you
shahee

On 6/4/18, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
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