What marks means clearly- you should use second equilibrium output file for final mdrun. i.e. posre_nvt
Sent from my iPhone > On 31-Mar-2016, at 12:17 am, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > Hi, > > The reasoning behind doing equilibration is covered in various tutorials, > which might be good background for you for other things too. There's no > point doing a second equilibration phase if you are going to start > production MD from the end point of the first equilibration phase. That's > pure waste. > > Mark > > On Wed, Mar 30, 2016 at 8:28 PM Pradip Kaur <kaur.pradip...@gmail.com> > wrote: > >> Sorry I didn't get you ...can you please explain me in details >>> On 30-Mar-2016 11:44 pm, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: >>> >>> Hi, >>> >>> Why would you do some equilibration, then some further equilibration, and >>> then start from the point before the further equilibration? >>> >>> Mark >>> >>> On Wed, Mar 30, 2016 at 8:12 PM Pradip Kaur <kaur.pradip...@gmail.com> >>> wrote: >>> >>>> but i have one question when i m running md.mdp which file should i >> use >>> as >>>> input file ,posre_npt.pdb or posre_nvt.pdb ? >>>> >>>> On 30 March 2016 at 23:40, Pradip Kaur <kaur.pradip...@gmail.com> >> wrote: >>>> >>>>> thanks so much >>>>> >>>>>> On 30 March 2016 at 21:33, Mark Abraham <mark.j.abra...@gmail.com> >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> The purpose of these equilibration phases is to allow the system to >>>> relax >>>>>> to the desired temperature and pressure. Since you observed that >> this >>>>>> happened before starting your production MD ;-) then there's no >> issue. >>>> But >>>>>> in many cases you'll have an easier life if you do it the other way >>>>>> around. >>>>>> >>>>>> Mark >>>>>> >>>>>> On Wed, Mar 30, 2016 at 5:23 PM Pradip Kaur < >> kaur.pradip...@gmail.com >>>> >>>>>> wrote: >>>>>> >>>>>>> i have run posre_npt.mdp first and then posre_nvt.mdp by mistake >> but >>>> now >>>>>>> going through gromacs manual i found that posre_nvt.mdp is first >> run >>>> and >>>>>>> then posre_npt.mdp, but i have already started md.mdp run with >>>>>>> posre_nvt.pdb (which was last generated pdb file after mdrun of >>>>>>> posre_nvt.mdp ) there is no error till now, should i need to stop >> my >>>>>> run or >>>>>>> continue with it ? >>>>>>> -- >>>>>>> Gromacs Users mailing list >>>>>>> >>>>>>> * Please search the archive at >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List >> before >>>>>>> posting! >>>>>>> >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>>> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>> or >>>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>> posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or >>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.