For a detailed description of how to set up protein simulation, I recomend you to read the Martini Tutorial on http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html there you will find step by step instructions along with some explanations of what you are actually doing. In this case you only want to build a water box around your protein. For that you will use editconf and a vdw distance of 0.19.
Regards Cesar 2009/12/17 rasoul nasiri <nasiri1...@gmail.com> > yes, I know there will be limitation for modeling of Folding/Unfolding > proteins with MARtini CGFF if I want to look at complete folding/unfolding > mechanism of proteins but I want to find out localized regions of the > protein (e.g. the C- or N-termini) that they have contribution to the > denaturation mechanism. > My question is about vdwd in beads of water. Is it OK if I select distances > of 0.15-0.20nm as vdwd of water beads in CGMD simulation or I have to > reconstruct the system in smaller vdw distance of the water beads for doing > my purpose. and Which commands of Gromacs can do it? > > Best regards > Rasoul > > On Thu, Dec 17, 2009 at 5:03 PM, César Ávila <clav...@gmail.com> wrote: > >> I suggest you read the original paper for Martini Protein FF. I think it >> is not suitable for your purpouse. >> >> 2009/12/17 rasoul nasiri <nasiri1...@gmail.com> >> >>> Hi, >>> >>> My purpose is finding of denaturation mechanism of proteins with MArtini >>> CGFF by Gromacs. >>> I mean after filling box in which there are beads of protein from water >>> beads with suitable van der wall distance (larger than 0.105nm), when I want >>> to start production phase, first switch back to the smaller radius of van >>> der waals of the water beads, then I will continue CGMD simulation. Is it >>> possible I reduce this radius? Which commands of Gromacs suit can do it? >>> >>> Rasoul >>> >>> >>> On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham >>> <mark.abra...@anu.edu.au>wrote: >>> >>>> rasoul nasiri wrote: >>>> >>>>> greetings GMX users, >>>>> >>>>> When I use genbox command for filling solvent in CGMD simulation with >>>>> Gromacs suit, I must use a larger van der Waals distance to avoid crashes. >>>>> when I use default value (0.105nm), system will crash. Which distance is >>>>> suitable for performing CGMD simulation. I used 0.15 or 0.2nm as >>>>> distances. >>>>> Are those OK? >>>>> >>>> >>>> Read up on your forcefield and find out how "large" the particles tend >>>> to be. It only has to be good enough, not perfect. >>>> >>>> >>>> I have to switch back to the smaller radius afterward, Is it correct? >>>>> >>>> >>>> Changing what for what purpose? >>>> >>>> >>>> if yes, How can I do it? I tried with editconf but could not. >>>>> >>>> >>>> I don't know what you mean. >>>> >>>> Mark >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search before >>>> posting! >>>> Please don't post (un)subscribe requests to the list. Use the www >>>> interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>> >>> >>> -- >>> >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> -- >> >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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