Thank Justin ! :-)
On Fri, Jan 11, 2013 at 5:26 PM, Justin Lemkul <[email protected]> wrote: > > > On 1/10/13 11:37 PM, Kieu Thu Nguyen wrote: > >> Thank Justin and Peter so much ! >> Can i make a new box (it's size is not a multiples of the size of the >> previous box) from a smaller lipid bilayer box ? >> >> I don't see genconf -nbox can do that. >> >> >> > genbox -cs old_lipids.gro -box x y z -o new_lipids.gro > > Just make sure you get a sensible number of lipids per leaflet. > > -Justin > > > >> On Fri, Jan 11, 2013 at 9:20 AM, Peter Lai <[email protected]> wrote: >> >> Kieu Thu Nguyen <[email protected]> wrote: >>> >>> Dear All, >>>> >>>> I see in MD simulations, the number of lipids is 128 or multiples of >>>> 128. >>>> Can someone tell me why ? >>>> Whether can i choose another number of lipids ? >>>> >>>> Thanks in advance ! >>>> KT >>>> -- >>>> 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> >>>> >>> >>> probably because they are using original 128-lipid coordinates from >>> someone like tieleman or klauda. You can use any arbitrary # of lipids >>> appropriate to the size of your intended system (like scaling it so that >>> an >>> embedded protein is shielded by lipids from its periodic image) >>> -- >>> Sent from my Android phone with K-9 Mail. Please excuse my brevity. >>> -- >>> 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> >>> >>> > -- > ==============================**========== > > 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
