Dear Cesar, Thank you for your reply, There are two different kind of water gro in this site (one of them is water.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html and another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html . Is there difference between them? Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script?
Another question; How can I change secondary structure information during CGMD simulation, If I want to perform CGMD simulation for finding of the folding/unfolding mechanism in proteins completely? Because Martini CGFF consider fix it. Cheers Rasoul On Fri, Dec 18, 2009 at 9:02 PM, César Ávila <clav...@gmail.com> wrote: > For a detailed description of how to set up protein simulation, I recommend > you to read the Martini Tutorial on > http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html<http://md.chem.rug.nl/%7Emarrink/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 >> > > > -- > 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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