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I have experience calculating molecular properties (mostly DFT). However, I would like to spend some time on molecular dynamics methods. I would like to ask your advice to direct me towards a program with which to calculate systems such as the annealing of a benzene molecule surrounded by a hundred water molecules.

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    $\begingroup$ This question from matter modeling SE might be helpful: mattermodeling.stackexchange.com/q/6143 $\endgroup$ Jun 17 at 5:31
  • $\begingroup$ Do you mean simulated annealing? You can use Gromacs (gromacs.org). Gromacs is quite easy to use. Also have a look at this post: mattermodeling.stackexchange.com/questions/4341/… I have done MD simulations of small molecules in gromacs, so I can write an answer on that if you want. I haven't done annealing so I can't really write about that. $\endgroup$
    – S R Maiti
    Jun 17 at 9:48
  • $\begingroup$ Nisarg Bhavsar, thanks, I will dive a little bit into NAMD and see if I can get something running, I see there are some tutorials on youtube, for example, youtube.com/watch?v=IArpsQsZ95U seems good! Shoubhik R Maiti thank you for pointing out Gromacs, also here I could dive into maybe looking at some tutorials will be useful: youtube.com/watch?v=rYZ1p5lXNyc&t=1s. $\endgroup$
    – user55257
    Jun 17 at 16:40
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    $\begingroup$ @PaulPerkele In my personal experience, learning gromacs was easier than learning NAMD (in fact right now I am trying to learn that). However, you may find the other one easier. Yes youtube tutorials are helpful. Do keep in mind though that for small molecules, you usually get parameters/topology from servers like swissparam.ch or from softwares (because you need general forcefield). As an aside, if you are responding to a comment on this site, make sure to tag them with an @ $\endgroup$
    – S R Maiti
    Jun 17 at 20:35

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