Re: [gmx-users] How to extend my incompleted simulation? (not extend a completed one)

[Alex]

Sorry, didn't notice the cpt files weren't yet generated. Justin is 
always right about everything.


Alex

On 12/29/2016 1:58 PM, Zhang, Cheng wrote:

Hi Justin,

Thank you very much. It worked as you said []


Yes, I was only using 10 min in the beginning, so no cpt file could be 
generated.


Yours sincerely

Cheng


From: Zhang, Cheng
Sent: 29 December 2016 19:02:47
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: How to extend my incompleted simulation? (not extend a completed 
one)


Hi Alex,

Thank you. I tested "mdrun_mpi -deffnm md_0_1 -cpi state.cpt -append". However, 
I still ONLY got the four files WITHOUT cpt file.

) md_0_1.trr
) md_0_1.xtc
) md_0_1.edr
) md_0_1.log


I know the link 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations,

but is it for extending a completed job? In my case, I want to continue a 
incompleted job.


Thank you.


Yours sincerely

Cheng



From: Zhang, Cheng
Sent: 29 December 2016 18:23
To: gromacs.org_gmx-users@maillist.sys.kth.se
Cc: Zhang, Cheng
Subject: How to extend my incompleted simulation? (not extend a completed one)

Dear Gromacs,
I would like to extend my simulation.

200 ns was put in the "md.mdp" file, which was used to build "md_0_1.tpr".

Then, I use "mdrun -deffnm md_0_1" to submit "md_0_1.tpr".

Due to the limitation on our cluster, only 5 ns (for example) was simulated when the job 
finishes. The "md_0_1.tpr" file is NOT changed, and I got other new files but 
WITHOUT a cpt file (why?):
) md_0_1.trr
) md_0_1.xtc
) md_0_1.edr
) md_0_1.log

So I want to continue the simulation from the end of 5 ns. How should I do this?

I am not quite sure if I understand correctly from 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations, and I also 
feel this link does not address my problem, as the tpr file was not changed in 
my case.

Thank you.

Yours sincerely
Cheng





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Re: [gmx-users] How to extend my incompleted simulation? (not extend a completed one)

[Zhang, Cheng]

Hi Justin,

Thank you very much. It worked as you said []


Yes, I was only using 10 min in the beginning, so no cpt file could be 
generated.


Yours sincerely

Cheng


From: Zhang, Cheng
Sent: 29 December 2016 19:02:47
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: How to extend my incompleted simulation? (not extend a completed 
one)


Hi Alex,

Thank you. I tested "mdrun_mpi -deffnm md_0_1 -cpi state.cpt -append". However, 
I still ONLY got the four files WITHOUT cpt file.

) md_0_1.trr
) md_0_1.xtc
) md_0_1.edr
) md_0_1.log


I know the link 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations,

but is it for extending a completed job? In my case, I want to continue a 
incompleted job.


Thank you.


Yours sincerely

Cheng



From: Zhang, Cheng
Sent: 29 December 2016 18:23
To: gromacs.org_gmx-users@maillist.sys.kth.se
Cc: Zhang, Cheng
Subject: How to extend my incompleted simulation? (not extend a completed one)

Dear Gromacs,
I would like to extend my simulation.

200 ns was put in the "md.mdp" file, which was used to build "md_0_1.tpr".

Then, I use "mdrun -deffnm md_0_1" to submit "md_0_1.tpr".

Due to the limitation on our cluster, only 5 ns (for example) was simulated 
when the job finishes. The "md_0_1.tpr" file is NOT changed, and I got other 
new files but WITHOUT a cpt file (why?):
) md_0_1.trr
) md_0_1.xtc
) md_0_1.edr
) md_0_1.log

So I want to continue the simulation from the end of 5 ns. How should I do this?

I am not quite sure if I understand correctly from 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations, and I also 
feel this link does not address my problem, as the tpr file was not changed in 
my case.

Thank you.

Yours sincerely
Cheng

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Re: [gmx-users] How to extend my incompleted simulation? (not extend a completed one)

[Justin Lemkul]

On 12/29/16 2:02 PM, Zhang, Cheng wrote:

Hi Alex,

Thank you. I tested "mdrun_mpi -deffnm md_0_1 -cpi state.cpt -append". However, 
I still ONLY got the four files WITHOUT cpt file.

) md_0_1.trr
) md_0_1.xtc
) md_0_1.edr
) md_0_1.log


I know the link 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations,

but is it for extending a completed job? In my case, I want to continue a 
incompleted job.



If you have no .cpt file, then you can only restart the job from the beginning. 
Your previous command of "mdrun -deffnm md_0_1" will not have produced anything 
called "state.cpt" so your above command will only start over from the beginning 
of the simulation (and the .log file should note this, otherwise check 
stdout/stderr).


Any run terminated prematurely can be continued simply by adding "-cpi -append" 
to the previous command, assuming a .cpt file is present.  If one is not 
present, then either the run crashed before writing it (again, check the .log or 
stdout/stderr for obvious error messages) or the cluster cut the job off before 
the -cpt interval (default: 15 minutes) was reached.


-Justin



Thank you.


Yours sincerely

Cheng



From: Zhang, Cheng
Sent: 29 December 2016 18:23
To: gromacs.org_gmx-users@maillist.sys.kth.se
Cc: Zhang, Cheng
Subject: How to extend my incompleted simulation? (not extend a completed one)

Dear Gromacs,
I would like to extend my simulation.

200 ns was put in the "md.mdp" file, which was used to build "md_0_1.tpr".

Then, I use "mdrun -deffnm md_0_1" to submit "md_0_1.tpr".

Due to the limitation on our cluster, only 5 ns (for example) was simulated when the job 
finishes. The "md_0_1.tpr" file is NOT changed, and I got other new files but 
WITHOUT a cpt file (why?):
) md_0_1.trr
) md_0_1.xtc
) md_0_1.edr
) md_0_1.log

So I want to continue the simulation from the end of 5 ns. How should I do this?

I am not quite sure if I understand correctly from 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations, and I also 
feel this link does not address my problem, as the tpr file was not changed in 
my case.

Thank you.

Yours sincerely
Cheng



--
==

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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Re: [gmx-users] How to extend my incompleted simulation? (not extend a completed one)

[Zhang, Cheng]

Hi Alex,

Thank you. I tested "mdrun_mpi -deffnm md_0_1 -cpi state.cpt -append". However, 
I still ONLY got the four files WITHOUT cpt file.

) md_0_1.trr
) md_0_1.xtc
) md_0_1.edr
) md_0_1.log


I know the link 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations,

but is it for extending a completed job? In my case, I want to continue a 
incompleted job.


Thank you.


Yours sincerely

Cheng



From: Zhang, Cheng
Sent: 29 December 2016 18:23
To: gromacs.org_gmx-users@maillist.sys.kth.se
Cc: Zhang, Cheng
Subject: How to extend my incompleted simulation? (not extend a completed one)

Dear Gromacs,
I would like to extend my simulation.

200 ns was put in the "md.mdp" file, which was used to build "md_0_1.tpr".

Then, I use "mdrun -deffnm md_0_1" to submit "md_0_1.tpr".

Due to the limitation on our cluster, only 5 ns (for example) was simulated 
when the job finishes. The "md_0_1.tpr" file is NOT changed, and I got other 
new files but WITHOUT a cpt file (why?):
) md_0_1.trr
) md_0_1.xtc
) md_0_1.edr
) md_0_1.log

So I want to continue the simulation from the end of 5 ns. How should I do this?

I am not quite sure if I understand correctly from 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations, and I also 
feel this link does not address my problem, as the tpr file was not changed in 
my case.

Thank you.

Yours sincerely
Cheng

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Re: [gmx-users] How to extend my incompleted simulation? (not extend a completed one)

[Alex]

add "-cpi state.cpt -append " into your mdrun command and submit it.
This is useful:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

Alex

On Dec 29, 2016 11:24 AM, "Zhang, Cheng"  wrote:

> Dear Gromacs,
> I would like to extend my simulation.
>
> 200 ns was put in the "md.mdp" file, which was used to build "md_0_1.tpr".
>
> Then, I use "mdrun -deffnm md_0_1" to submit "md_0_1.tpr".
>
> Due to the limitation on our cluster, only 5 ns (for example) was
> simulated when the job finishes. The "md_0_1.tpr" file is NOT changed, and
> I got other new files but WITHOUT a cpt file (why?):
> ) md_0_1.trr
> ) md_0_1.xtc
> ) md_0_1.edr
> ) md_0_1.log
>
> So I want to continue the simulation from the end of 5 ns. How should I do
> this?
>
> I am not quite sure if I understand correctly from http://www.gromacs.org/
> Documentation/How-tos/Extending_Simulations, and I also feel this link
> does not address my problem, as the tpr file was not changed in my case.
>
> Thank you.
>
> Yours sincerely
> Cheng
>
> --
> 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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