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

[sun]

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 ?
>>>>>>> --
>>>>>>> Gromacs Users mailing list
>>>>>>> 
>>>>>>> * Please search the archive at
>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>> before
>>>>>>> posting!
>>>>>>> 
>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>> 
>>>>>>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>> or
>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>> 
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>> 
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>> 
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>> --
>>>> Gromacs Users mailing list
>>>> 
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>> 
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>> 
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>> 
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.