On Mon, May 14, 2018 at 7:10 AM, Salman Zarrini <[email protected]> wrote: > Probably the "gmx make_ndx" can help to bundle 4 water molecules. To bundle molecules in gromacs you will have to put a virtual bond between them.
Christoph > > 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. -- Christoph Junghans Web: http://www.compphys.de -- 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.
