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 <[email protected]> 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 <[email protected]> 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 >>> -- >>> gmx-users mailing list gmx-users at gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-request at gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
