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 <[email protected]> > 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 <[email protected]>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 [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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