Result analysis of QM/MM output from Gromacs_CP2K

QM/MM for Biomolecular Simulation
#21

At first you should compile GROMACS-CP2K.
https://manual.gromacs.org/current/install-guide/index.html#building-with-cp2k-qm-mm-support

If you dont know what to do that, please ask someone around who has experience in building programs from source files. As it requires access to you machine to help.

Second, you are using wrong tutorial, correct one is
https://github.com/bioexcel/gromacs-2022-cp2k-tutorial

#22

Okay sir
Thankyou so much.

#23

Dear Dmitry,
I successfully run TD-DFT calculation with gmx_cp2k interface. I got spec.xvg. Also, I would like to have HOMO-LUMO (ground and excited) state electron density image from TD-DFT.

Previously, you have suggested me for using the below keyword for homo-lumo in the section to &FORCE_EVAL / &DFT:-

&PRINT
   &MO_CUBES                 
    NHOMO 1
    NLUMO 1
  &END MO_CUBES
&END PRINT

Now, my query is where I can insert these keywords in .inp file for TD-DFT HOMO-LUMO?

With regards,
Ranabir

#24

Hello sir
I’m following the tutorial link which you shared,
Go to nma directory:
cd nma
this is the first step of it, I wrote cd nma but error showed that there is no nma directory. I cretaed a directory by naming it as nma and then i moved on to the second step “gmx pdb2gmx -f nma.pdb” if i write this code I should get the forcefild and water model to choose but i’m not getting it…
can you please help me out …

Screenshot (238)
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#25

You did not downloaded tutorial

#26

I’m following this tutorial link sir…

#27

@Pallavi,
Kindly learn first how to use Linux os. Then try to install and run gromacs properly. Gromacs-CP2k QMMM simulation is a very advanced stage. So please 1st learn the basics.

#28

Dear Dmitry,

I am happy to inform you that I successfully run gromacs_CP2k QM/MM in my institute’s supercomputer.

Now, I am facing some doubts about setting up QM/MM files.
First, I have minimized and equilibrated (MM-NVT, MM-NPT) my QM/MM system (DNA-Ligand in water) then I have performed QM-MM-EM, QM-MM-NVT as per your tutorial. Is QM-MM-NPT not needed before the final QM/MM production run?

Also, it will be very helpful if you could provide me with the necessary mdp files to set up QM/MM simulation.

With regards,
Ranabir

#30

Hi Ranabir,

NPT is possible, but strictly saying you will not get better results with pressure coupling in QMMM.
For the QMMM I would suggest to use just NVT.

Best,
Dmitry

#31

Thanks, Dmitry for your kind suggestion.