Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Mark Abraham]

Yes

On Tue, 26 Apr 2016 08:12 Husen R  wrote:

> Hi,
>
>
> Thanks for your reply.
>
> There is no state.cpt or state_prev.cpt file.
>
> In equilibration part 1 the resulting checkpoint files : nvt.cpt and
> nvt_prev.cpt
> In equilibration part 2 the resulting checkpoint files : npt.cpt and
> npt_prev.cpt
> In Production MD the resulting checkpoint files  : md_0_1.cpt and
> md_0_1_prev.cpt
>
> is this because of -deffnm option ?
> I just want to make sure.
>
> Regards,
>
>
> Husen
>
>
> On Tue, Apr 26, 2016 at 11:45 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > On Tue, 26 Apr 2016 06:19 Husen R  wrote:
> >
> > > Hi all,
> > >
> > > I tried to run this gromacs tutorial (
> > >
> > >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
> > > )
> > > in order to understand how checkpoint/restart works in Gromacs-5.1.2.
> > >
> > > Based on running that tutorial I found that mdrun automatically
> > checkpoint
> > > even though I didn't specify -cpt option (based on mdrun manual page,
> by
> > > default checkpoint every 15 minutes)
> > >
> >
> > Yes, as that webpage suggests.
> >
> > 1. What if I specify -cpt option with a value longer than or smaller than
> > > 15 minutes ? does -cpt value will automatically override the default ?
> > >
> >
> > Yes, the default is used when you don't supply a value. But usually you
> > don't need to think about this.
> >
> > 2. I run the following command to restart production MD step (using
> SLURM)
> > > from checkpoint file. md_0_1_prev.cpt is .cpt file resulting from
> > previous
> > > mdrun execution. is my command right ? I just want to make sure.
> > >
> >
> > Not quite. From that webpage: "Note that mdrun will write state.cpt and
> > state_prev.cpt files. As you can see from their time stamps, one was
> > written approximately at the checkpoint interval before the other (15
> mins
> > by default). Or you can use gmxcheck to see what is in them." You want to
> > follow the examples there and do your restart from the most recent file,
> > which is state.cpt. The older file is just kept for safety. Your command
> > will lead to wasting 15 minutes of simulation.
> >
> > Mark
> >
> > #!/bin/bash
> > > #SBATCH -J Lysozyme
> > > #SBATCH -o md-%j.out
> > > #SBATCH -A necis
> > > #SBATCH -N 3
> > > #SBATCH -n 24
> > > #SBATCH --time=144:00:00
> > > #SBATCH --mail-user=hus...@gmail.com
> > > #SBATCH --mail-type=begin
> > > #SBATCH --mail-type=end
> > >
> > > mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1
> > >
> > >
> > > Thank you in advance
> > >
> > > Regards,
> > >
> > >
> > > Husen
> > >
> > >
> > > On Sun, Apr 24, 2016 at 7:57 PM, Husen R  wrote:
> > >
> > > > Hi,
> > > >
> > > > Thanks a lot !
> > > > I'll try it,..
> > > >
> > > > Regards,
> > > >
> > > >
> > > > Husen
> > > >
> > > > On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul 
> > wrote:
> > > >
> > > >>
> > > >>
> > > >> On 4/24/16 12:04 AM, Husen R wrote:
> > > >>
> > > >>> Dear all,
> > > >>>
> > > >>> is there any complete documentation discussing checkpoint/restart
> in
> > > >>> Gromacs-5.1.2 ?
> > > >>> I found this link that discuss checkpoint (
> > > >>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
> )
> > > and
> > > >>> this link that discuss restart (
> > > >>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but
> > these
> > > >>> are
> > > >>> not specifically for gromacs 5.1.2.
> > > >>>
> > > >>>
> > > >> There are no differences for 5.1.2, so that information is all
> > relevant.
> > > >>
> > > >> -Justin
> > > >>
> > > >> --
> > > >> ==
> > > >>
> > > >> Justin A. Lemkul, Ph.D.
> > > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > > >>
> > > >> Department of Pharmaceutical Sciences
> > > >> School of Pharmacy
> > > >> Health Sciences Facility II, Room 629
> > > >> University of Maryland, Baltimore
> > > >> 20 Penn St.
> > > >> Baltimore, MD 21201
> > > >>
> > > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > >> http://mackerell.umaryland.edu/~jalemkul
> > > >>
> > > >> ==
> > > >> --
> > > >> 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
> > 

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Husen R]

Hi,


Thanks for your reply.

There is no state.cpt or state_prev.cpt file.

In equilibration part 1 the resulting checkpoint files : nvt.cpt and
nvt_prev.cpt
In equilibration part 2 the resulting checkpoint files : npt.cpt and
npt_prev.cpt
In Production MD the resulting checkpoint files  : md_0_1.cpt and
md_0_1_prev.cpt

is this because of -deffnm option ?
I just want to make sure.

Regards,


Husen


On Tue, Apr 26, 2016 at 11:45 AM, Mark Abraham 
wrote:

> Hi,
>
> On Tue, 26 Apr 2016 06:19 Husen R  wrote:
>
> > Hi all,
> >
> > I tried to run this gromacs tutorial (
> >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
> > )
> > in order to understand how checkpoint/restart works in Gromacs-5.1.2.
> >
> > Based on running that tutorial I found that mdrun automatically
> checkpoint
> > even though I didn't specify -cpt option (based on mdrun manual page, by
> > default checkpoint every 15 minutes)
> >
>
> Yes, as that webpage suggests.
>
> 1. What if I specify -cpt option with a value longer than or smaller than
> > 15 minutes ? does -cpt value will automatically override the default ?
> >
>
> Yes, the default is used when you don't supply a value. But usually you
> don't need to think about this.
>
> 2. I run the following command to restart production MD step (using SLURM)
> > from checkpoint file. md_0_1_prev.cpt is .cpt file resulting from
> previous
> > mdrun execution. is my command right ? I just want to make sure.
> >
>
> Not quite. From that webpage: "Note that mdrun will write state.cpt and
> state_prev.cpt files. As you can see from their time stamps, one was
> written approximately at the checkpoint interval before the other (15 mins
> by default). Or you can use gmxcheck to see what is in them." You want to
> follow the examples there and do your restart from the most recent file,
> which is state.cpt. The older file is just kept for safety. Your command
> will lead to wasting 15 minutes of simulation.
>
> Mark
>
> #!/bin/bash
> > #SBATCH -J Lysozyme
> > #SBATCH -o md-%j.out
> > #SBATCH -A necis
> > #SBATCH -N 3
> > #SBATCH -n 24
> > #SBATCH --time=144:00:00
> > #SBATCH --mail-user=hus...@gmail.com
> > #SBATCH --mail-type=begin
> > #SBATCH --mail-type=end
> >
> > mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1
> >
> >
> > Thank you in advance
> >
> > Regards,
> >
> >
> > Husen
> >
> >
> > On Sun, Apr 24, 2016 at 7:57 PM, Husen R  wrote:
> >
> > > Hi,
> > >
> > > Thanks a lot !
> > > I'll try it,..
> > >
> > > Regards,
> > >
> > >
> > > Husen
> > >
> > > On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul 
> wrote:
> > >
> > >>
> > >>
> > >> On 4/24/16 12:04 AM, Husen R wrote:
> > >>
> > >>> Dear all,
> > >>>
> > >>> is there any complete documentation discussing checkpoint/restart in
> > >>> Gromacs-5.1.2 ?
> > >>> I found this link that discuss checkpoint (
> > >>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations)
> > and
> > >>> this link that discuss restart (
> > >>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but
> these
> > >>> are
> > >>> not specifically for gromacs 5.1.2.
> > >>>
> > >>>
> > >> There are no differences for 5.1.2, so that information is all
> relevant.
> > >>
> > >> -Justin
> > >>
> > >> --
> > >> ==
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >>
> > >> Department of Pharmaceutical Sciences
> > >> School of Pharmacy
> > >> Health Sciences Facility II, Room 629
> > >> University of Maryland, Baltimore
> > >> 20 Penn St.
> > >> Baltimore, MD 21201
> > >>
> > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > >> http://mackerell.umaryland.edu/~jalemkul
> > >>
> > >> ==
> > >> --
> > >> 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
> >
> > * 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
>
> * For (un)subscribe 

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Mark Abraham]

Hi,

On Tue, 26 Apr 2016 06:19 Husen R  wrote:

> Hi all,
>
> I tried to run this gromacs tutorial (
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
> )
> in order to understand how checkpoint/restart works in Gromacs-5.1.2.
>
> Based on running that tutorial I found that mdrun automatically checkpoint
> even though I didn't specify -cpt option (based on mdrun manual page, by
> default checkpoint every 15 minutes)
>

Yes, as that webpage suggests.

1. What if I specify -cpt option with a value longer than or smaller than
> 15 minutes ? does -cpt value will automatically override the default ?
>

Yes, the default is used when you don't supply a value. But usually you
don't need to think about this.

2. I run the following command to restart production MD step (using SLURM)
> from checkpoint file. md_0_1_prev.cpt is .cpt file resulting from previous
> mdrun execution. is my command right ? I just want to make sure.
>

Not quite. From that webpage: "Note that mdrun will write state.cpt and
state_prev.cpt files. As you can see from their time stamps, one was
written approximately at the checkpoint interval before the other (15 mins
by default). Or you can use gmxcheck to see what is in them." You want to
follow the examples there and do your restart from the most recent file,
which is state.cpt. The older file is just kept for safety. Your command
will lead to wasting 15 minutes of simulation.

Mark

#!/bin/bash
> #SBATCH -J Lysozyme
> #SBATCH -o md-%j.out
> #SBATCH -A necis
> #SBATCH -N 3
> #SBATCH -n 24
> #SBATCH --time=144:00:00
> #SBATCH --mail-user=hus...@gmail.com
> #SBATCH --mail-type=begin
> #SBATCH --mail-type=end
>
> mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1
>
>
> Thank you in advance
>
> Regards,
>
>
> Husen
>
>
> On Sun, Apr 24, 2016 at 7:57 PM, Husen R  wrote:
>
> > Hi,
> >
> > Thanks a lot !
> > I'll try it,..
> >
> > Regards,
> >
> >
> > Husen
> >
> > On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 4/24/16 12:04 AM, Husen R wrote:
> >>
> >>> Dear all,
> >>>
> >>> is there any complete documentation discussing checkpoint/restart in
> >>> Gromacs-5.1.2 ?
> >>> I found this link that discuss checkpoint (
> >>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations)
> and
> >>> this link that discuss restart (
> >>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but these
> >>> are
> >>> not specifically for gromacs 5.1.2.
> >>>
> >>>
> >> There are no differences for 5.1.2, so that information is all relevant.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==
> >> --
> >> 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
>
> * 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] Gromacs-5.1.2 Checkpoint/restart example

[Husen R]

Hi all,

I tried to run this gromacs tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html)
in order to understand how checkpoint/restart works in Gromacs-5.1.2.

Based on running that tutorial I found that mdrun automatically checkpoint
even though I didn't specify -cpt option (based on mdrun manual page, by
default checkpoint every 15 minutes)

1. What if I specify -cpt option with a value longer than or smaller than
15 minutes ? does -cpt value will automatically override the default ?

2. I run the following command to restart production MD step (using SLURM)
from checkpoint file. md_0_1_prev.cpt is .cpt file resulting from previous
mdrun execution. is my command right ? I just want to make sure.

#!/bin/bash
#SBATCH -J Lysozyme
#SBATCH -o md-%j.out
#SBATCH -A necis
#SBATCH -N 3
#SBATCH -n 24
#SBATCH --time=144:00:00
#SBATCH --mail-user=hus...@gmail.com
#SBATCH --mail-type=begin
#SBATCH --mail-type=end

mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1


Thank you in advance

Regards,


Husen


On Sun, Apr 24, 2016 at 7:57 PM, Husen R  wrote:

> Hi,
>
> Thanks a lot !
> I'll try it,..
>
> Regards,
>
>
> Husen
>
> On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 4/24/16 12:04 AM, Husen R wrote:
>>
>>> Dear all,
>>>
>>> is there any complete documentation discussing checkpoint/restart in
>>> Gromacs-5.1.2 ?
>>> I found this link that discuss checkpoint (
>>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and
>>> this link that discuss restart (
>>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but these
>>> are
>>> not specifically for gromacs 5.1.2.
>>>
>>>
>> There are no differences for 5.1.2, so that information is all relevant.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> 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] Gromacs-5.1.2 Checkpoint/restart example

[Husen R]

Hi,

Thanks a lot !
I'll try it,..

Regards,


Husen

On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul  wrote:

>
>
> On 4/24/16 12:04 AM, Husen R wrote:
>
>> Dear all,
>>
>> is there any complete documentation discussing checkpoint/restart in
>> Gromacs-5.1.2 ?
>> I found this link that discuss checkpoint (
>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and
>> this link that discuss restart (
>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but these
>> are
>> not specifically for gromacs 5.1.2.
>>
>>
> There are no differences for 5.1.2, so that information is all relevant.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> 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] Gromacs-5.1.2 Checkpoint/restart example

[Justin Lemkul]

On 4/24/16 12:04 AM, Husen R wrote:

Dear all,

is there any complete documentation discussing checkpoint/restart in
Gromacs-5.1.2 ?
I found this link that discuss checkpoint (
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and
this link that discuss restart (
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but these are
not specifically for gromacs 5.1.2.



There are no differences for 5.1.2, so that information is all relevant.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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