Alain-chavanieu commented 1 year ago

Hello

This summer we ran several dynamics (openMM/charmm) using your notebook on google colab. As said in a previous mail, Many thanks for that. Now, we ll have to run coarse-grained dynamic (Martini 3.0.0) with a system.top as that one (below) and (e.g.) such /bin

Is there any possibility a google colab notebook will be available in weeks coming , May be there is little interest for that ? However running a dynamic simultation on google colab is very confortable for us (low CPU, no GPU in the lab)

Thank you for your time and help

Alain

!/bin/csh #

www.charmm-gui.org)

#

1) Use Gromacs 5.1 or newer to run these simulations

#

Minimization

setenv GMX_MAXCONSTRWARN -1

step4.0 - soft-core minimization

gmx grompp -f step4.0_minimization.mdp -o step4.0_minimization.tpr -c step3_charmm2gmx.pdb -r step3_charmm2gmx.pdb -p system.top -n index.ndx gmx mdrun -deffnm step4.0_minimization

step4.1

gmx grompp -f step4.1_minimization.mdp -o step4.1_minimization.tpr -c step4.0_minimization.gro -r step3_charmm2gmx.pdb -p system.top -n index.ndx gmx mdrun -deffnm step4.1_minimization unsetenv GMX_MAXCONSTRWARN

Equilibration

gmx grompp -f step4.2_equilibration.mdp -o step4.2_equilibration.tpr -c step4.1_minimization.gro -r step3_charmm2gmx.pdb -p system.top -n index.ndx gmx mdrun -deffnm step4.2_equilibration

Production

gmx grompp -f step5_production.mdp -o step5_production.tpr -c step4.2_equilibration.gro -p system.top -n index.ndx gmx mdrun -deffnm step5_production

system.top

include "toppar/martini_v3.0.0.itp"

include "toppar/martini_v3.0.0_ions_v1.itp"

include "toppar/martini_v3.0.0_nucleobases_v1.itp"

include "toppar/martini_v3.0.0_phospholipids_v1.itp"

include "toppar/martini_v3.0.0_phospholipids_v1_matthieu.itp"

include "toppar/martini_v3.0.0_small_molecules_v1.itp"

include "toppar/martini_v3.0.0_solvents_v1.itp"

include "toppar/martini_v3.0.0_sugars_v1.itp"

include "p15c2_proa.itp"

include "p15c2_prob.itp"

include "p15c2_proc.itp"

[ system ] ; name Martini system

[ molecules ] ; name number PROA 1 PROB 1 PROC 1 W 38366 NA 428 CL 426

pablo-arantes commented 1 year ago

Hi @Alain-chavanieu,

Sorry for my delay. Unfortunately, it's still not possible to use coarse-grained models (Martini, SIRAH, etc) on OpenMM engine. As our notebooks are using OpenMM engine to run the molecular dynamics simulations, we cannot use coarse-grained models yet. One suggestion is installing Gromacs on Google Colab and run your coarse-grained simulations there. Follow a video where they have shown how to install and run Gromacs on Colab: https://www.youtube.com/watch?v=HDlO13gvgsY&ab_channel=SelfStudy

I hope it helps.

Thank you.

Best,

Pablo