I am so grateful for your help sincerely
On Mon, Jan 21, 2013 at 5:24 AM, Justin Lemkul <[email protected]> wrote: > > > On 1/20/13 8:34 PM, Mehdi Bagherpour wrote: > >> excuse me Dear Justin >> >> I could not understand exactly what to do? >> My simulation system is DNA in water. >> >> > The -center option is convenient when you have to center a single molecule > within a unit cell. If you have two molecules or more that you wish to > center, it can be more complex than you might expect. Consider the > following boxes. Both represent a double-stranded DNA molecule that is > considered centered in the box: > > __________ > | | > | | > | XX | > | | > |__________| > > __________ > | | > | | > X X > | | > |__________| > > In both cases, the geometric center coincides with the center of the box, > even though the two molecules are split via PBC. My previous suggestion > (and there are more detailed examples of what to do by reading the wiki > site and checking the mailing list archive) is to make an index group that > represents a more well-defined center. In the case of a protein dimer, > maybe this would be a few residues that are at the protein-protein > interface, thus enforcing a more strict criterion for centering. For a DNA > molecule, maybe center on only one strand, such that the other strand is > repositioned based on a more intuitive reference. Even centering on a > single nucleotide would probably work. Otherwise, trjconv has a variety of > options (again, check the wiki for a workflow) that can deal with these > situations. Often times, a single command is insufficient to achieve the > representation you want. Other options like -fit could also be useful > here, but not in conjunction with -pbc. > > -Justin > > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
