[gmx-users] regarding rmsd calculation

[SHAHEE ISLAM]

sorry to forget about the recentering of the .xtc file.after getting
the dynamic.xtc file i just recenter the .xtc file before doing rmsd
analysis.

On 6/5/18, SHAHEE ISLAM <islamshahee at gmail.com> wrote:
> 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
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>