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

2016-03-31 Thread Tsjerk Wassenaar 
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"  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 
> 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 
> > wrote:
> >
> >> Sorry I didn't get you  ...can you please explain me in details
> >>> On 30-Mar-2016 11:44 pm, "Mark Abraham" 
> 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 
> >>> 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 
> >> wrote:
> 
> > thanks so much
> >
> >> On 30 March 2016 at 21:33, Mark Abraham 
> > 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.pradip...@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-requ...@gromacs.org.
> >> --
> >> Gromacs Users mailing list
> >>
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> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
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Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

2016-03-31 Thread 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  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"  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 
>> 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 
>> > wrote:
>> >
>> >> Sorry I didn't get you  ...can you please explain me in details
>> >>> On 30-Mar-2016 11:44 pm, "Mark Abraham" 
>> 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 > >
>> >>> 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 
>> >> wrote:
>> 
>> > thanks so much
>> >
>> >> On 30 March 2016 at 21:33, Mark Abraham 
>> > 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.pradip...@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-requ...@gromacs.org.
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
>> >>
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>>  --
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>>  * Please search the archive at
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>>  posting!
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Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

2016-03-30 Thread 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  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 
> wrote:
> 
>> Sorry I didn't get you  ...can you please explain me in details
>>> On 30-Mar-2016 11:44 pm, "Mark Abraham"  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 
>>> 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 
>> wrote:
 
> thanks so much
> 
>> On 30 March 2016 at 21:33, Mark Abraham 
> 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.pradip...@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-requ...@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
>> 
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>> send a mail to gmx-users-requ...@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-requ...@gromacs.org.
>>> --
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Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

2016-03-30 Thread 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 
wrote:

> Sorry I didn't get you  ...can you please explain me in details
> On 30-Mar-2016 11:44 pm, "Mark Abraham"  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 
> > 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 
> wrote:
> > >
> > > > thanks so much
> > > >
> > > > On 30 March 2016 at 21:33, Mark Abraham 
> > > 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.pradip...@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-requ...@gromacs.org.
> > > >> >
> > > >> --
> > > >> Gromacs Users mailing list
> > > >>
> > > >> * Please search the archive at
> > > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > >> posting!
> > > >>
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> or
> > > >> send a mail to gmx-users-requ...@gromacs.org.
> > > >>
> > > >
> > > >
> > > --
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Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

2016-03-30 Thread Pradip Kaur 
Sorry I didn't get you  ...can you please explain me in details
On 30-Mar-2016 11:44 pm, "Mark Abraham"  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 
> 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  wrote:
> >
> > > thanks so much
> > >
> > > On 30 March 2016 at 21:33, Mark Abraham 
> > 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  >
> > >> 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-requ...@gromacs.org.
> > >> >
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
> > >>
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> > >>
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> > >> send a mail to gmx-users-requ...@gromacs.org.
> > >>
> > >
> > >
> > --
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Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

2016-03-30 Thread Mark Abraham 
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 
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  wrote:
>
> > thanks so much
> >
> > On 30 March 2016 at 21:33, Mark Abraham 
> 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 
> >> 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!
> >> >
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> >> > send a mail to gmx-users-requ...@gromacs.org.
> >> >
> >> --
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> >
> >
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Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

2016-03-30 Thread Pradip Kaur 
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  wrote:

> thanks so much
>
> On 30 March 2016 at 21:33, Mark Abraham  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 
>> 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-requ...@gromacs.org.
>> >
>> --
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>>
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>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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>>
>
>
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Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

2016-03-30 Thread Pradip Kaur 
thanks so much

On 30 March 2016 at 21:33, Mark Abraham  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 
> 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!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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