Sorry, i have one more question : Does genbox make new box that the area per lipid is unchange (the same with the old box) ?
On Fri, Jan 11, 2013 at 7:04 PM, Kieu Thu Nguyen <[email protected]>wrote: > 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
