[gmx-users] regarding rmsd calculation

[Justin Lemkul]

On 6/5/18 3:05 AM, SHAHEE ISLAM 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.

Yes, you failed to provide a checkpoint file to -t when invoking grompp 
the second time, so your system did not preserve its state. You 
shouldn't use grompp to extend a simulation unless you need to change 
something about the settings; the easiest way to extend is with 
convert-tpr (tpbconv in old versions). Instructions are on the GROMACS 
website.

-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
http://www.thelemkullab.com

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