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

Fri Apr 1 07:48:22 CEST 2016

No, what Mark means is that if you equilibrated temperature AND pressure
(NpT) there's no point in an NVT step, in which the pressure may go off
again, even though it's unlikely to matter much, because the volume is
already within proper range.

However, there's the 'posre' part still, which suggests that the
equilibrations were run with position restraints. Before production, there
should be some equilibration without these.

In the end, in this case it doesn't matter much. If the production
simulation runs, it runs. Do take care to cut off enough of the first part
to account for long term relaxation effects.

I think the biggest concern is that the worry suggests a lack of insight in
the process and theory of MD. Please do follow Marks advise and run through
a number of tutorials.

Cheers,

Tsjerk
On Mar 31, 2016 05:45, "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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