[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

[Pradip Kaur]

Hi ,
I started mdrun with posre_npt .mdp  and I have ignored posre_nvt.mdp
becoz  posre_nvt equilibrium is unnecessary if it is run after
posre_nvt.mdp
So ,as I already have run em.mdp  first  then posre_npt and finally
posre_nvt .So in order to avoid further problems I took posre_npt .pdb as
input (which was generated after running mdrun of em.mdp )for mdrun of
MD.mdp  .

Please correct me if I m wrong.
On 31-Mar-2016 9:15 am, "sun" <sun.iba2 at gmail.com> wrote:

> 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.abraham at 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.pradip253 at 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.abraham at 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.pradip253 at 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.pradip253 at gmail.com>
> >> wrote:
> >>>>
> >>>>> thanks so much
> >>>>>
> >>>>>> On 30 March 2016 at 21:33, Mark Abraham <mark.j.abraham at 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.pradip253 at 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 ?
> >>>>>>> --
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