Computational Chemistry 3.9 - MD Program

[@andrecarvalho8679]

Amazing work, gave me inspiration to try building a suite like this. Thank you very much!!!

[@TMPChem]

Thanks Andre. Please do.

[@dylanogden95]

this is awesome!!! We use NAMD in our lab but seeing it broken down in python is really cool

[@TMPChem]

Nice. The real C++ / Fortran implementation is of course going to be more systematic and performance tuned, but this program is designed for almost-beginners to be able to go through the code and read it.

[@aonoymousandy7467]

great video, it's good to know that there are people working on MD simulation programs because the AMBER program really sucks.

[@TMPChem]

Lol. Every piece of software has it's pros and cons. I haven't actually used the full proprietary version of AMBER, just the free AMBERTools subset of it. I quickly got bored reading through documentation and just decided to read the original paper and implement the force field myself as an exercise, and thus the progenitor to this toy script was born. That was fine because I only needed to compute non-bonded energies for a small set of single-point energy calculations on a handful of small molecules. If you're doing serious MD work I *highly* *highly* (did I mention *highly*?) suggest investing the time to use a professional, production-level code, rather than the poorly-tested late-night rambling code of some random guy on the internet, but I suppose this could be useful for understanding some of the basics before graduating to the real thing. It certainly won't be nearly as informative browsing through the source code tree of endless subdirectories of Fortran and C header files.

[@yhk6187]

Is there any way to use your repository on my notebook? There are too many errors everytime I try to do the samething you showed on the video. This time:--------------------------------------------------------------------------- NameError Traceback (most recent call last) ~\desktop\mm.py in 30 31 # Print results to screen. ---> 32 molecule.PrintData() 33 ~\desktop\mmlib\molecule.py in PrintData(self) 632 """Print energy / geometry / topology data of molecule to screen.""" 633 self.PrintEnergy() --> 634 self.PrintGeom() 635 self.PrintBonds() 636 self.PrintAngles() ~\desktop\mmlib\molecule.py in PrintGeom(self) 644 def PrintGeom(self): 645 """Print geometry data of molecule to screen.""" --> 646 print(fileio.GetPrintGeomString(self.atoms)) 647 648 def PrintBonds(self): ~\desktop\mmlib\fileio.py in GetPrintGeomString(atoms) 827 """ 828 if not atoms: --> 829 return _ATOM_PRINT_ABSENT 830 831 string = [_GetHeaderString(_GEOM_PRINT_HEADER, _GEOM_PRINT_BANNER_CHARS, NameError: name '_ATOM_PRINT_ABSENT' is not defined

[@alirezasadeghifar3815]

Great work! Can we have access to this code? Can we use that in our research and cite you?

[@MohitKumar-hi2tk]

What is meaning of simulation