On Mon, May 14, 2018, 05:27 Alex <[email protected]> wrote: > 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? > VOTCA doesn't support mapping multiple molecules into one. You would have to bundle them up first to do such kind of mappings.
Christoph 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. > -- 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.
