[gmx-users] Re: Can Gromacs functions be called by some other codes?

[Tsjerk Wassenaar]

Hey Kai,

I would still argue that, from your description, the best solution is
a (bash) wrapper script, containing the workflow. If you do that
properly, it will result in a much more flexible, readable and
maintainable solution. If you end up writing shell calls in C or
Python, you have to sit back for a while and consider if that's really
what you need or that you'd be better of doing shell scripting.

Cheers,

Tsjerk


On Tue, Jun 12, 2012 at 9:48 PM, Da-Wei Li <lidawei at gmail.com> wrote:
> In your own code, you should have a system call function, which can be
> used to run any command in your system. Using C as example, you can
> write source code like this.
>
> /*******************************************************/
> system("g_rms -s xx.tpr -f xx.trr -o rmsd.xvg");
> read in file rmsd.xvg to get the RMSD.
>
> if(RMSD>3A)
>      system("mdrun -s **********"");
> else
>      printf("very good, stable MD\n");
>
> /*****************************************************/
>
> dawei
>
> On Tue, Jun 12, 2012 at 3:28 PM, Bao Kai <paeanball at gmail.com> wrote:
>> Hi, Dawei,
>>
>> We have some other codes. Sometimes, we can not know the range of the
>> physical parameters we need in advance. When we do the simulation, we
>> may find some required properties are not ready, then we need to run
>> some MD simulations to get the values of the properties. Then the
>> simulation can continue.
>>
>> We want to do the MD simulations only when necessary and we want to do
>> the MD simulations automatically.
>>
>> So I am wondering if we can complete some MD simulations and get the
>> required analysis results by calling the functions inside Gromacs
>> library.
>>
>> Thank you very much.
>>
>> Best Regards,
>> Kai
>>
>>
>> >From your description, why not just write a script to run various
>> Gromacs programs (MD, analysis, etc)?
>>
>> dawei
>>
>> On Tue, Jun 12, 2012 at 2:43 PM, Bao Kai <paeanball at gmail.com> wrote:
>>> Hi, all,
>>>
>>> I am wondering if Gromacs functions can be called by some other codes.
>>>  I know we get some library files and header files and we can write
>>> our own analysis tools.
>>>
>>> But I still wonder to what extent the gromacs can be coupled to other codes.
>>>
>>> For example, can we just generate the topology and .gro and .mdp files
>>> ( we can write our own code to do that ), then call the the functions
>>> or procedures in Gromacs library to complete the MD simulation, and
>>> then call some functions to return the analysis results, such as
>>> density, viscosity, and etc.
>>>
>>> Thank you very much.
>>>
>>> Best Regards,
>>> Kai
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands