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
