On Mon, May 14, 2018 at 07:40 Christoph Junghans <[email protected]> wrote:
> > > 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. > Hi Christoph, I know, that is why I wanted to use martinize.py following your old advice in the mailing list. What is the correct command of martinize.py -f AA-water.gro -x CG-P4-water.gro ... ? Regarding the bonding, how can I do that? Thanks. Alex > > 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. > -- Best regards, Salman Zarrini -- 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.
