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

[Pradip Kaur]

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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