Convert calculations from Gromacs to hoomd

[Hoomd user Den]

Hello, all! I have calculated molecular dynamics in Gromacs. Now I want use hoomd. How I can use similar parameters and files with coords and velocities for system which I use in Gromacs? What do I need? Is there someone who has some experience?

[Hoomd user Den]

I will glad for any help. Thanks!

четверг, 8 сентября 2016 г., 12:51:06 UTC+3 пользователь Hoomd user Den написал:

[Jens Glaser]

Hi,

for the coordinates and velocities,  you’ll have to write a (e.g. python) converter from .gro to .gsd or .xml yourself. Shouldn’t be

too hard.

Also, we are working on adding support for some all-atom force fields to HOOMD-blue.

Right now, many things such as various bonded interactions or distance constraints are already

supported. Notably missing are scaled exclusion as they are e.g. used in GROMOS.

If you want to live on the bleeding edge, have an eye out for this pull request

https://bitbucket.org/glotzer/hoomd-blue/pull-requests/248/pair-potentials-between-special-particle/diff

to support these scaled exclusions.

Also of interest:

https://bitbucket.org/jens_glaser/gmx_to_hoomd

for conversion of force field and topology files. I am not providing support for the latter script as of now

- use at your own risk.

Jens

On Sep 8, 2016, at 5:51 AM, Hoomd user Den <dv.il...@physics.msu.ru> wrote:

Hello, all! I have calculated molecular dynamics in Gromacs. Now I want use hoomd. How I can use similar parameters and files with coords and velocities for system which I use in Gromacs? What do I need? Is there someone who has some experience?

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[Hoomd user Den]

So for using hoomd molecular dynamics I need gsd file format with positions and types of particles and also any topology file, and python running file. Is it true?

четверг, 8 сентября 2016 г., 12:51:06 UTC+3 пользователь Hoomd user Den написал:

Hello, all! I have calculated molecular dynamics in Gromacs. Now I want use hoomd. How I can use similar parameters and files with coords and velocities for system which I use in Gromacs? What do I need? Is there someone who has some experience?

[Jens Glaser]

On Sep 8, 2016, at 8:51 AM, Hoomd user Den <dv.il...@physics.msu.ru> wrote:

So for using hoomd molecular dynamics I need gsd file format with positions and types of particles and also any topology file, and python running file. Is it true?

Yes.

You can however also initialize your system using python via snapshots.

J

четверг, 8 сентября 2016 г., 12:51:06 UTC+3 пользователь Hoomd user Den написал:

Hello, all! I have calculated molecular dynamics in Gromacs. Now I want use hoomd. How I can use similar parameters and files with coords and velocities for system which I use in Gromacs? What do I need? Is there someone who has some experience?

[Hoomd user Den]

Jens, thank you)  If I will initialize system via snapshot, I must use this http://gsd.readthedocs.io/en/latest/hoomd-examples.html#hoomd-examples ? I must create python file with this instructions? And this file will be "two in one", topology and position? 

четверг, 8 сентября 2016 г., 12:51:06 UTC+3 пользователь Hoomd user Den написал:

Hello, all! I have calculated molecular dynamics in Gromacs. Now I want use hoomd. How I can use similar parameters and files with coords and velocities for system which I use in Gromacs? What do I need? Is there someone who has some experience?

[Joshua Anderson]

You are free to create input files by whatever method you prefer. I would recommend using the gsd python package to write files, but that is just a recommendation. Regarding position vs topology, hoomd does not support reading a separate file for topology separate from particle properties. If you wish to create such a file format, you can implement a reader in python that creates a snapshot data structure.

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
Phone: 734-647-8244
http://www-personal.umich.edu/~joaander/

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