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

[Mark Abraham]

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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