Quoting Ricardo Soares <[email protected]>: > noob noob wrote: > > > > Dear all, > > > > I am new about MD simulation and I have some questions about the box > > size. > > > > I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5 > > nm ) but now I change to a bigger molecules and increase the number of > > molecules. So,the new system cannot fix into the previous box. > > Therefore, I tried to Increase my box to a bigger one ( 20 nm x 20 nm > > x 20 nm) which can fix the system nicely. > > > > So, is it compulsory to use certain box size in our system? or we just use > > any box size which our molecules can fix into it, then perform MD? > > > Sorry, I didn't see this other question of yours. > If you use a box that is much larger than the main molecule, you will > need lots of water, which will be time-consuming. Otherwise, if you use > a very small box, it may compromise the free movement of the protein. > So i say the best option is to scale the box size according to your > specific molecule size. This is done within the editconf program. (see > the gromacs manual for further reference). >
In addition, you need to consider cutoff lengths and periodic boundary conditions/minimum image convention. Some textbook reading is in order. -Justin > Cheers, > > Ricardo. > > > > Sorry for the "stupid" questions. > > > > thanks for the comments. > > > > > > Alvin Chan. > > ------------------------------------------------------------------------ > > check out the rest of the Windows Live. More than mailWindows Live > > goes way beyond your inbox. More than messages > > <http://www.microsoft.com/windows/windowslive/> > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.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 > > > -- > ___________________________________________________________ > > Ricardo Oliveira dos Santos Soares > Post-graduation Student in Biological Physics > University of Sao Paulo - USP > Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP > Phone: 55 (16) 3602-4840 > Curriculum Lattes - http://lattes.cnpq.br/0777038258459931 > ___________________________________________________________ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [email protected] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.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
