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

[Pradip Kaur]

 can i use only one equilibrium(only posre_npt.mdp)  i.e if after em.mdp if
i run posre_npt file and use the output of posre_npt file for final mdrun?


On 31 March 2016 at 20:32, Pradip Kaur <kaur.pradip253 at gmail.com> wrote:

> 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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>