Martini water

[Alexander Alexander]

Dear all,
I was wondering what the correct usage of martinize.py is for mapping a atomistic water.gro file to the P4 water martini coarse grained?
The "martinize.py -f AA-water.gro -x CG-water.gro ... " gives me only a box of the system.

How about when I have system including two type of molecules and water, like " AA-water-mol1-mol2.gro"? I know the mapping (mapping.xml) of the mol1 and mol2 in VOTCA.

Thank you.
Alex

[Tristan Bereau]

Dear Alex,

As far as I know, `martinize.py` is only meant to be used to coarse grain proteins. It won't give you an interface to coarse grain anything else:

http://www.cgmartini.nl/index.php/tools2/proteins-and-bilayers/204-martinize

Since you're eluding to the idea of combining Martini water with a structure-based CG model, beware that this can lead to major inconsistencies.

Best,

Tristan

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[Alex]

Hi Tristan,

Thanks for your comment.

I know the difference between the two structure and free energy based models.

Actually the mapping of 1-water-mol:1-bead of VOTCA CG is not useful for me here and I need to have something like the P4 Martini water 4-water-mols:1-beads.

Any way, do you know how to mapp the AA-water.gro to the CG-P4-martini.gro? 

Thanks.

Alex

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[Christoph Junghans]

On Mon, May 14, 2018, 05:27 Alex <alexand...@gmail.com> wrote:

Hi Tristan,

Thanks for your comment.

I know the difference between the two structure and free energy based models.

Actually the mapping of 1-water-mol:1-bead of VOTCA CG is not useful for me here and I need to have something like the P4 Martini water 4-water-mols:1-beads.

Any way, do you know how to mapp the AA-water.gro to the CG-P4-martini.gro?

VOTCA doesn't support mapping multiple molecules into one. You would have to bundle them up first to do such kind of mappings.

Christoph

[Salman Zarrini]

On Mon, May 14, 2018 at 07:40 Christoph Junghans <jung...@votca.org> wrote:

On Mon, May 14, 2018, 05:27 Alex <alexand...@gmail.com> wrote:

Hi Tristan,

Thanks for your comment.

I know the difference between the two structure and free energy based models.

Actually the mapping of 1-water-mol:1-bead of VOTCA CG is not useful for me here and I need to have something like the P4 Martini water 4-water-mols:1-beads.

Any way, do you know how to mapp the AA-water.gro to the CG-P4-martini.gro?

VOTCA doesn't support mapping multiple molecules into one. You would have to bundle them up first to do such kind of mappings.

Hi Christoph,

I know, that is why I wanted to use martinize.py following your old advice in the mailing list.

What is the correct command of martinize.py -f AA-water.gro -x CG-P4-water.gro ... ?

Regarding the bonding, how can I do that?

Thanks.

Alex

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Best regards,

Salman Zarrini

[Salman Zarrini]

Probably the "gmx make_ndx" can help to bundle 4 water molecules.

Best regards,

Salman Zarrini

Christoph

Thanks.

Alex

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[Christoph Junghans]

On Mon, May 14, 2018, 05:49 Salman Zarrini <salman....@gmail.com> wrote:

On Mon, May 14, 2018 at 07:40 Christoph Junghans <jung...@votca.org> wrote:

On Mon, May 14, 2018, 05:27 Alex <alexand...@gmail.com> wrote:

Hi Tristan,

Thanks for your comment.

I know the difference between the two structure and free energy based models.

Actually the mapping of 1-water-mol:1-bead of VOTCA CG is not useful for me here and I need to have something like the P4 Martini water 4-water-mols:1-beads.

Any way, do you know how to mapp the AA-water.gro to the CG-P4-martini.gro?

VOTCA doesn't support mapping multiple molecules into one. You would have to bundle them up first to do such kind of mappings.

Hi Christoph,

I know, that is why I wanted to use martinize.py following your old advice in the mailing list.

What is the correct command of martinize.py -f AA-water.gro -x CG-P4-water.gro ... ?

I don't know! That is a question for martini mailing list!

Christoph

[Christoph Junghans]

On Mon, May 14, 2018 at 7:10 AM, Salman Zarrini
<salman....@gmail.com> wrote:
> Probably the "gmx make_ndx" can help to bundle 4 water molecules.

To bundle molecules in gromacs you will have to put a virtual bond between them.

Christoph

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