<div dir="ltr"><p dir="ltr">Hi,</p>
<p dir="ltr">I am strongly in favour of a well developed comprehensive API. It really makes it possible to extend the functionality of GROMACS to applications that were not envisioned by the original developers.</p>
<p dir="ltr">In our case we wanted to develop a GCMC package that used MD as a configuration generator. GromPy was an excellent way to start but I soon realized that I needed do have a much more detailed control of GROMACS mechanisms. As I wanted to implement an OO approach we decided it would be better to start from scratch..</p>
<p dir="ltr">So, I extensively mapped, and extended, the existing API to python classes using ctypes. Using ctypeslib to automatically map required types and functions really made a difference in terms of developing time. The automatic code is not very pretty, but, at a development stage is good enough (can clean it latter).</p>
<p dir="ltr">We are now at the point of benchmarking the first GCMC simulations. The code performs standard GCMC simulations and also Continuous-Fractional-Component insertion. Reaction-Ensemble simulations are almost ready. We would like to present the code in the CCP5 conference in September.</p>
<p dir="ltr">We worked with the 4.6.5 version of GMX but will want to migrate to the C++ version of the code. I expect that a OO code will be much easier to integrate (mine is already OO) with. Still, I did not have the time to look at the new code, so I can't say anything yet.</p>
<p dir="ltr">One the biggest problems I had with the C code was that memory management was simply not there. I fully understand why. Structures were made once, used, and then the program finished, leaving the task of freeing memory to the OS. I needed to write "destructors" for most of those. I hope the C++ code, being OO, has destructors implemented. If not, I'll have to do it. ;-)</p>
<p>Thanks for all your hard work, GROMACS is GREAT!!</p><p><br></p><p>Kind regards,</p><p>Rui Fartaria</p><p>Research assistant</p><p>University of Edinburgh</p><p><br></p><p><br></p><p><br></p></div>