Justin A. Lemkul ha scritto: >> My aim is to re-implement a formerly standalone CG model by mean of gmx. >> It seems that gmx is well suited to the task; however I understand that >> there is an incredible number of pitfalls where a newbie fall in. >> >> I am currently reading and re-reading the manual, looking at the online >> docs and tutorials. But most of information, understandably, refer to >> all-atom modeling and there is little on how to build your own model >> on gmx. >> >> Maybe my googling skills are not as good as once they were -in this case >> can anyone point me to any page where this kind of task is documented? >> >> If such a page there isn't (and even if there is), I would appreciate a >> lot if anyone of you can share your wisdom on best practices, pitfalls, >> things to know etc. before diving head-on in such an endeavour. >> > > So, to clarify, this is an already-existing CG model that you simply > want to use for simulations in Gromacs? It is then rather easy. You > need to define all appropriate force field files (nb.itp, bon.itp, .atp, > etc), and perhaps .rtp files if you can also come up with a way to > define an appropriate CG input for pdb2gmx.
Yes. I know the specs of the cg model, and I want to re-implement it within gromacs. Actually it is a class of related models. I'd start from a very minimal one and then improve gradually. I understand I have to define all appropriate FF files, but I wonder what is the best way to do it, what documentation to learn by heart, what sanity checks... You make me optimist in saying "it is rather easy" , but science is always full of traps, especially for the newcomer... thanks! m. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
