[gmx-users] regarding rmsd calculation

Justin Lemkul jalemkul at vt.edu
Tue Jun 5 13:53:55 CEST 2018

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 



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


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