Script for cascade molecular dynamics

Question

[Samilla]

Hi! guys! I´m working with molecular dynamics and the thing is I have to do many replicas of an MD simulation for my molecule. Does anyone know about a script that could intercalate these simulations? I mean, soon as MD1 ended the MD2 started? Sort of cascading MD... Thanks for your attention in advance.

[fracarb8]

You need to be more specific about how you are currently running MDs. Which software are you using (GROMACS, AMBER, NAMD, other) ? Are you doing classical MD or REMD? Are you including the equilibration steps in your cascade? What you are asking can be as easy as concatenate few bash commands, to write a proper and complex pipeline.

[Samilla]

OK! I´m using classical MD, programmed by GROMACS. And I want to start the cascade from the last command

• gmx mdrun -v -deffnm

All the other steps were already programmed.

" What you are asking can be as easy as concatenate few bash commands, to write a proper and complex pipeline." Could you tell me how I can do this?

Thx