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

[Da-Wei Li]

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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