Hi Tristan, Thanks for your comment. I know the difference between the two structure and free energy based models. Actually the mapping of 1-water-mol:1-bead of VOTCA CG is not useful for me here and I need to have something like the P4 Martini water 4-water-mols:1-beads. Any way, do you know how to mapp the AA-water.gro to the CG-P4-martini.gro? Thanks. Alex
On Mon, May 14, 2018 at 02:29 Tristan Bereau <[email protected]> wrote: > Dear Alex, > > As far as I know, `martinize.py` is only meant to be used to coarse grain > proteins. It won't give you an interface to coarse grain anything else: > > > http://www.cgmartini.nl/index.php/tools2/proteins-and-bilayers/204-martinize > > Since you're eluding to the idea of combining Martini water with a > structure-based CG model, beware that this can lead to major > inconsistencies. > > Best, > Tristan > > On Mon, May 14, 2018 at 4:54 AM Alexander Alexander < > [email protected]> wrote: > >> Dear all, >> I was wondering what the correct usage of martinize.py is for mapping a >> atomistic water.gro file to the P4 water martini coarse grained? >> The "martinize.py -f AA-water.gro -x CG-water.gro ... " gives me only a >> box of the system. >> >> How about when I have system including two type of molecules and water, >> like " AA-water-mol1-mol2.gro"? I know the mapping (mapping.xml) of the >> mol1 and mol2 in VOTCA. >> >> Thank you. >> Alex >> >> -- >> > You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. > > >> To post to this group, send email to [email protected]. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. >> > -- > You received this message because you are subscribed to a topic in the > Google Groups "votca" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/votca/4lL_6eVOhHo/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
