Hello Gustaf,

Indeed we have to update the Martini tutorials to GROMACS 5+ some time soon. In short they all do work with GROMACS 5+, you just have to change the names of the GROMACS commands e.g. mdrun to gmx mdrun etc. The GROMACS website gives good directions on how to make the switch. The only other thing is that in GROMACS 5+ they are going to deprecate the use of the group neighbor scheme (which standard Martini used), I think you can still use it by explicitly adding "cutoff-scheme = group" to your .mdp files. But I would recommend using the new martini .mdp parameters that have been optimized to work with the Verlet scheme, see martini_v2.x_new-rf.mdp on: http://www.cgmartini.nl/index.php/force-field-parameters/input-parameters

There are also some posts discussing this one the Martini forum.

Cheers, Helgi

Hi Gustaf,

You can try using charmm gui for generating the inputs for gromacs if your system is a membrane protein system. It gives options for picking up different martini parameters. I have used it and it worked for me but I am not using gromacs 5.X instead I am using version-3.x. Good Luck with your experiment.

--

best,

Kalpana 

Thank you Kalpana, I will definitely have a look at the charm gui.

It seems that most of the tutorials and papers I've found uses gromacs versions < 4.X. Maybe I should take that as an indication.

Hello Gustaf,

Indeed we have to update the Martini tutorials to GROMACS 5+ some time soon. In short they all do work with GROMACS 5+, you just have to change the names of the GROMACS commands e.g. mdrun to gmx mdrun etc. The GROMACS website gives good directions on how to make the switch. The only other thing is that in GROMACS 5+ they are going to deprecate the use of the group neighbor scheme (which standard Martini used), I think you can still use it by explicitly adding "cutoff-scheme = group" to your .mdp files. But I would recommend using the new martini .mdp parameters that have been optimized to work with the Verlet scheme, see martini_v2.x_new-rf.mdp on: http://www.cgmartini.nl/index.php/force-field-parameters/input-parameters

There are also some posts discussing this one the Martini forum.

Cheers, Helgi

Hi Helgi

In the meanwhile I will keep trying. For the most part it seems to work in basically the same way, though there are some commands that are gone and have been replaced with new ones that have different command syntax and options, requiring a bit of work  in order to use the python scripts from the tutorial. 

For instance, g_bond has been replaced with gmx distance and while they seem able to perform the same tasks, the execution and options of these commands does not seem to be identical and therefore the commands from the tutorial leads to incorrect execution.

I'll try to figure it out and have a look at the forums. Thank you for your kind reply

Hi Helgi

Minimization.mdp file for Gromacs 5+ is not updated on the website. When it will be available? If you know the contents of the file can you please paste it here itself.

Thanks

Sorry for not getting back to you sooner, its been a while. Did you manage on your own?

Anyway, after posting this, I realized that gromac2016 was the version of gromacs that was up to date, not 5.x. I invested a lot of time and energy getting through one of the tutorials last year and I have save some of the documentation. The minimization.mdp file I ended up using looked like this:

   #include "martini_v2.1.itp"

   #include "martini_v2.0_lipids.itp"

   [ system ]

   DSPC BILAYER SELF-ASSEMBLY

   [ molecules ]

   DSPC 128

   W 768

and the command to execute became

   gmx grompp -f minimization.mdp -c waterbox.gro -p dspc.top -maxwarn 10 -o dspc-min-solvent.tpr -quiet -nocopyright

This is produced no errors though there were notes:

NOTE 1 [file minimization.mdp]:

The group cutoff scheme is deprecated since GROMACS 5.0 and will be

removed in a future release when all interaction forms are supported for

the verlet scheme. The verlet scheme already scales better, and it is

compatible with GPUs and other accelerators.

NOTE 2 [file minimization.mdp]:

The switch/shift interaction settings are just for compatibility; you

will get better performance from applying potential modifiers to your

interactions!

So this is not optimal and should likely be improved.