Thank Justin ! It is so hard to get the right APL in the new box (after genbox step) ! How can i predict the new box size (that made after energy minimization) ? The box is compressed after running EM.
On Sat, Jan 12, 2013 at 6:38 PM, Justin Lemkul <[email protected]> wrote: > > > On 1/12/13 6:17 AM, Kieu Thu Nguyen wrote: > >> Sorry, i have one more question : Does genbox make new box that the area >> per lipid is unchange (the same with the old box) ? >> >> > genbox reads in the old coordinates and uses them to build a grid within > the new box. It will not write partial molecules, so in the case of > lipids, you may be left with rather large voids in the new box. Thus you > would need fairly extensive equilibration to prepare the system and > hopefully achieve the proper APL. > > So no, genbox does not guarantee this for you. > > -Justin > > 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> >>>>>>> <htt**p://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> >>>>>>> <h**ttp://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> >>>>>>> <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> >>>>>> <htt**p://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> >>>>>> <h**ttp://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> >>>>>> <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://vt.edu/Pages/Personal/justin> >>>> <h**ttp://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> >>>> <htt**p://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<h**ttp://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> >>>> <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? 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