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 >
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