Probably the "gmx make_ndx" can help to bundle 4 water molecules.
Best regards, Salman Zarrini On Mon, May 14, 2018 at 7:49 AM, Salman Zarrini <[email protected]> wrote: > 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. >> > -- 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.
