Re: [gmx-users] checkpoint file

[rama david]

Hi  Juliette ,

If your data is more and because of that may be  -append not support you.

Then these may be help you ..

mdrun -v -deffnm use different name than previous -s your tpr file
-cpi cpt

See carefully the output and check the time  at which the run
start..Is the  starting time point matches your crash point.

lastly when run complete, use trajcat ( catenate two trajectory),
catenate two trajectory...(previous and latest)

you can also catenate edr file..

So 1st make clear that why run crash??? If no abnormality then proceed
further...

These is the way I tackle my crash run on Gromacs 4.5.4


With best wishes and regards,
Rama David
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Re: [gmx-users] checkpoint file

[Matthias Ernst]

Long story short: backup everything (since it's a backup, and hopefully 
you won't need it), then use the [whatever].cpt file. You don't want to 
do work twice, do you? If you use the [whatever]_prev.cpi file, you will 
calculate some frames *again* that are already there.
If you use an up-to-date version of Gromacs (4.5.5 is the most recent 
one), then the files will be continued and not overwritten. This is 
stated on the page you already found (hint: remaining output will be 
appended to the existing files (energy, trajectory, log, etc).)


Good luck,
Matthias

Am 13.08.2012 21:07, schrieb Juliette N.:

Hello all,

I am going to restart my crashed simulations, but I am not sure which
of  *_prev.cpt or *.cpt to use as they contain different written
frames.

  *_prev.cpt  Last frame -1 time 7462.900

  *.cptLast frame -1 time 7468.965

Also on the gmx site it is stated that :

Before doing anything, back up your files! Then use

mdrun -s topol.tpr -cpi state.cpt


What files do I need to back up? the edr. trr .. files that were
written before crash? Is the new run going to overwrite the old files?


Thanks,


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Re: [gmx-users] checkpoint file

[Juliette N.]

Thank you. I am using

 mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x  -cpi md_prev.cpt

but I dont get any output and the issued command terminates in the terminal.

Do I have to remove the -o -c -g -e -x flags from the command line?

Appreciate your help,


On 13 August 2012 15:28, Matthias Ernst matthias.ern...@student.kit.edu wrote:
 Long story short: backup everything (since it's a backup, and hopefully you
 won't need it), then use the [whatever].cpt file. You don't want to do work
 twice, do you? If you use the [whatever]_prev.cpi file, you will calculate
 some frames *again* that are already there.
 If you use an up-to-date version of Gromacs (4.5.5 is the most recent one),
 then the files will be continued and not overwritten. This is stated on the
 page you already found (hint: remaining output will be appended to the
 existing files (energy, trajectory, log, etc).)

 Good luck,
 Matthias

 Am 13.08.2012 21:07, schrieb Juliette N.:

 Hello all,

 I am going to restart my crashed simulations, but I am not sure which
 of  *_prev.cpt or *.cpt to use as they contain different written
 frames.

   *_prev.cpt  Last frame -1 time 7462.900

   *.cptLast frame -1 time 7468.965

 Also on the gmx site it is stated that :

 Before doing anything, back up your files! Then use

 mdrun -s topol.tpr -cpi state.cpt


 What files do I need to back up? the edr. trr .. files that were
 written before crash? Is the new run going to overwrite the old files?


 Thanks,


 --
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 http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] checkpoint file

[Justin Lemkul]

On 8/13/12 3:42 PM, Juliette N. wrote:

Thank you. I am using

  mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x  -cpi md_prev.cpt

but I dont get any output and the issued command terminates in the terminal.



Normally error messages are rather obvious.  Check your .log file carefully or 
any redirects from stderr/stdout.



Do I have to remove the -o -c -g -e -x flags from the command line?



No, but they're useless anyway since you're using -deffnm, which sets the 
default name for all input and output files.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] checkpoint file

[Matthias Ernst]

Am 13.08.2012 21:42, schrieb Juliette N.:

Thank you. I am using

  mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x  -cpi md_prev.cpt
I see a md_prev.cpt. If I presume correctly that this is for the 
continuation of the crashed run: Why and did you read what I wrote?




but I dont get any output and the issued command terminates in the terminal.

Do I have to remove the -o -c -g -e -x flags from the command line?

Appreciate your help,


On 13 August 2012 15:28, Matthias Ernst matthias.ern...@student.kit.edu wrote:

Long story short: backup everything (since it's a backup, and hopefully you
won't need it), then use the [whatever].cpt file. You don't want to do work
twice, do you? If you use the [whatever]_prev.cpi file, you will calculate
some frames *again* that are already there.
If you use an up-to-date version of Gromacs (4.5.5 is the most recent one),
then the files will be continued and not overwritten. This is stated on the
page you already found (hint: remaining output will be appended to the
existing files (energy, trajectory, log, etc).)

Good luck,
Matthias

Am 13.08.2012 21:07, schrieb Juliette N.:


Hello all,

I am going to restart my crashed simulations, but I am not sure which
of  *_prev.cpt or *.cpt to use as they contain different written
frames.

   *_prev.cpt  Last frame -1 time 7462.900

   *.cptLast frame -1 time 7468.965

Also on the gmx site it is stated that :

Before doing anything, back up your files! Then use

mdrun -s topol.tpr -cpi state.cpt


What files do I need to back up? the edr. trr .. files that were
written before crash? Is the new run going to overwrite the old files?


Thanks,


--
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Re: [gmx-users] checkpoint file

[Juliette N.]

Yes this is to continue a crashed run, but I dont know why my runs
crash at the very beginnig of the simulation. I am using 4.5.4 so
-append should work by default. I tried a simulation from time zero
and it works as before (   mpirun -np 8 mdrun_mpi -deffnm md -s -o -c
-g -e -x ) but as soon as I include the -cpi flag the it doesn work
and  I get:

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

While as I said if I try to start from the very beginning it doesnt crash...

Any ideas..

Thanks


On 13 August 2012 15:51, Matthias Ernst matthias.ern...@student.kit.edu wrote:


 Am 13.08.2012 21:42, schrieb Juliette N.:

 Thank you. I am using

   mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x  -cpi md_prev.cpt

 I see a md_prev.cpt. If I presume correctly that this is for the
 continuation of the crashed run: Why and did you read what I wrote?



 but I dont get any output and the issued command terminates in the
 terminal.

 Do I have to remove the -o -c -g -e -x flags from the command line?

 Appreciate your help,


 On 13 August 2012 15:28, Matthias Ernst matthias.ern...@student.kit.edu
 wrote:

 Long story short: backup everything (since it's a backup, and hopefully
 you
 won't need it), then use the [whatever].cpt file. You don't want to do
 work
 twice, do you? If you use the [whatever]_prev.cpi file, you will
 calculate
 some frames *again* that are already there.
 If you use an up-to-date version of Gromacs (4.5.5 is the most recent
 one),
 then the files will be continued and not overwritten. This is stated on
 the
 page you already found (hint: remaining output will be appended to the
 existing files (energy, trajectory, log, etc).)

 Good luck,
 Matthias

 Am 13.08.2012 21:07, schrieb Juliette N.:

 Hello all,

 I am going to restart my crashed simulations, but I am not sure which
 of  *_prev.cpt or *.cpt to use as they contain different written
 frames.

*_prev.cpt  Last frame -1 time 7462.900

*.cptLast frame -1 time 7468.965

 Also on the gmx site it is stated that :

 Before doing anything, back up your files! Then use

 mdrun -s topol.tpr -cpi state.cpt


 What files do I need to back up? the edr. trr .. files that were
 written before crash? Is the new run going to overwrite the old files?


 Thanks,


 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 * Only plain text messages are allowed!
 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] checkpoint file

[Justin Lemkul]

On 8/13/12 4:08 PM, Juliette N. wrote:

Yes this is to continue a crashed run, but I dont know why my runs
crash at the very beginnig of the simulation. I am using 4.5.4 so
-append should work by default. I tried a simulation from time zero
and it works as before (   mpirun -np 8 mdrun_mpi -deffnm md -s -o -c
-g -e -x ) but as soon as I include the -cpi flag the it doesn work
and  I get:

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

While as I said if I try to start from the very beginning it doesnt crash...

Any ideas..



Before OpenMPI exits, there should be a reason why mdrun is exiting that is 
printed to the same stream.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] checkpoint file

[Juliette N.]

Sorry Justin, but I dont see whats happening...
Do I have to remove mpi or -np from the line while using -cpi *.cpt  ?

mdrun -deffnm md -s -o -c -g -e -x -cpi  output

Thanks!


On 13 August 2012 16:10, Justin Lemkul jalem...@vt.edu wrote:


 On 8/13/12 4:08 PM, Juliette N. wrote:

 Yes this is to continue a crashed run, but I dont know why my runs
 crash at the very beginnig of the simulation. I am using 4.5.4 so
 -append should work by default. I tried a simulation from time zero
 and it works as before (   mpirun -np 8 mdrun_mpi -deffnm md -s -o -c
 -g -e -x ) but as soon as I include the -cpi flag the it doesn work
 and  I get:

 NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
 You may or may not see output from other processes, depending on
 exactly when Open MPI kills them.

 While as I said if I try to start from the very beginning it doesnt
 crash...

 Any ideas..


 Before OpenMPI exits, there should be a reason why mdrun is exiting that is
 printed to the same stream.


 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
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Re: [gmx-users] checkpoint file

[Justin Lemkul]

On 8/13/12 4:16 PM, Juliette N. wrote:

Sorry Justin, but I dont see whats happening...
Do I have to remove mpi or -np from the line while using -cpi *.cpt  ?



No, you don't. All you should need (provided the .cpt file is valid, which it 
appears to be from the gmxcheck output from before) is:


mpirun -np 8 mdrun_mpi -deffnm md -cpi -append

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] checkpoint file

[Juliette N.]

I am using the same line, but it crashes...Is that because my trr
files is big that it cand append the files? It was ~ 40 GB when crash
happened...

I am using 4.5.4. I tried both with and without -append.



On 13 August 2012 16:19, Justin Lemkul jalem...@vt.edu wrote:


 On 8/13/12 4:16 PM, Juliette N. wrote:

 Sorry Justin, but I dont see whats happening...
 Do I have to remove mpi or -np from the line while using -cpi *.cpt  ?


 No, you don't. All you should need (provided the .cpt file is valid, which
 it appears to be from the gmxcheck output from before) is:

 mpirun -np 8 mdrun_mpi -deffnm md -cpi -append


 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
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Re: [gmx-users] checkpoint file

[Justin Lemkul]

On 8/13/12 4:34 PM, Juliette N. wrote:

I am using the same line, but it crashes...Is that because my trr
files is big that it cand append the files? It was ~ 40 GB when crash
happened...

I am using 4.5.4. I tried both with and without -append.



If it fails with and without the -append option, then that's clearly not the 
problem.  There would be a distinct error printed if there were a problem with 
appending to any file.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] checkpoint file

[Juliette N.]

Thanks, maybe I should re start ... :(



On 13 August 2012 16:36, Justin Lemkul jalem...@vt.edu wrote:


 On 8/13/12 4:34 PM, Juliette N. wrote:

 I am using the same line, but it crashes...Is that because my trr
 files is big that it cand append the files? It was ~ 40 GB when crash
 happened...

 I am using 4.5.4. I tried both with and without -append.


 If it fails with and without the -append option, then that's clearly not the
 problem.  There would be a distinct error printed if there were a problem
 with appending to any file.


 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] checkpoint file

[Juliette N.]

Hi all,

My cpt file  doesnt contain any information?!!

 gmxcheck -f md.cpt  gives the following:

Checking file md.cpt

# Atoms  20688
Last frame -1 time 7468.965


Item#frames Timestep (ps)
Step 1
Time 1
Lambda   1
Coords   1
Velocities   1
Forces   0
Box  1

Is this a valid cpt file?


Thank you,

On 13 August 2012 16:36, Justin Lemkul jalem...@vt.edu wrote:


 On 8/13/12 4:34 PM, Juliette N. wrote:

 I am using the same line, but it crashes...Is that because my trr
 files is big that it cand append the files? It was ~ 40 GB when crash
 happened...

 I am using 4.5.4. I tried both with and without -append.


 If it fails with and without the -append option, then that's clearly not the
 problem.  There would be a distinct error printed if there were a problem
 with appending to any file.


 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 * Only plain text messages are allowed!
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Re: [gmx-users] checkpoint file

[Justin Lemkul]

On 8/13/12 4:54 PM, Juliette N. wrote:

Hi all,

My cpt file  doesnt contain any information?!!



Sure it does.


  gmxcheck -f md.cpt  gives the following:

Checking file md.cpt

# Atoms  20688
Last frame -1 time 7468.965


Item#frames Timestep (ps)
Step 1
Time 1
Lambda   1
Coords   1
Velocities   1
Forces   0
Box  1

Is this a valid cpt file?



All indications are that it is.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] checkpoint file

[Juliette N.]

All right, but I was expecting some more information reflecting the
last state of the system, e.g, velocities...

Thank you,


On 13 August 2012 17:04, Justin Lemkul jalem...@vt.edu wrote:


 On 8/13/12 4:54 PM, Juliette N. wrote:

 Hi all,

 My cpt file  doesnt contain any information?!!


 Sure it does.


   gmxcheck -f md.cpt  gives the following:

 Checking file md.cpt

 # Atoms  20688
 Last frame -1 time 7468.965


 Item#frames Timestep (ps)
 Step 1
 Time 1
 Lambda   1
 Coords   1
 Velocities   1
 Forces   0
 Box  1

 Is this a valid cpt file?


 All indications are that it is.


 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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Re: [gmx-users] checkpoint file

[Justin Lemkul]

On 8/13/12 5:10 PM, Juliette N. wrote:

All right, but I was expecting some more information reflecting the
last state of the system, e.g, velocities...



gmxcheck verifies the integrity of the file.  gmxdump will produce more detailed 
information, not that it's of any particular use in this case.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] checkpoint file

[Mark Abraham]

On 14/08/2012 6:08 AM, Juliette N. wrote:

Yes this is to continue a crashed run, but I dont know why my runs
crash at the very beginnig of the simulation.


You have to look at the stderr, stdout and .log file for information. 
You can't solve the problem without that.


Mark


  I am using 4.5.4 so
-append should work by default. I tried a simulation from time zero
and it works as before (   mpirun -np 8 mdrun_mpi -deffnm md -s -o -c
-g -e -x ) but as soon as I include the -cpi flag the it doesn work
and  I get:

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

While as I said if I try to start from the very beginning it doesnt crash...

Any ideas..

Thanks


On 13 August 2012 15:51, Matthias Ernst matthias.ern...@student.kit.edu wrote:


Am 13.08.2012 21:42, schrieb Juliette N.:


Thank you. I am using

   mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x  -cpi md_prev.cpt

I see a md_prev.cpt. If I presume correctly that this is for the
continuation of the crashed run: Why and did you read what I wrote?



but I dont get any output and the issued command terminates in the
terminal.

Do I have to remove the -o -c -g -e -x flags from the command line?

Appreciate your help,


On 13 August 2012 15:28, Matthias Ernst matthias.ern...@student.kit.edu
wrote:

Long story short: backup everything (since it's a backup, and hopefully
you
won't need it), then use the [whatever].cpt file. You don't want to do
work
twice, do you? If you use the [whatever]_prev.cpi file, you will
calculate
some frames *again* that are already there.
If you use an up-to-date version of Gromacs (4.5.5 is the most recent
one),
then the files will be continued and not overwritten. This is stated on
the
page you already found (hint: remaining output will be appended to the
existing files (energy, trajectory, log, etc).)

Good luck,
Matthias

Am 13.08.2012 21:07, schrieb Juliette N.:


Hello all,

I am going to restart my crashed simulations, but I am not sure which
of  *_prev.cpt or *.cpt to use as they contain different written
frames.

*_prev.cpt  Last frame -1 time 7462.900

*.cptLast frame -1 time 7468.965

Also on the gmx site it is stated that :

Before doing anything, back up your files! Then use

mdrun -s topol.tpr -cpi state.cpt


What files do I need to back up? the edr. trr .. files that were
written before crash? Is the new run going to overwrite the old files?


Thanks,


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Re: [gmx-users] checkpoint file and *.gro -- energy calculation

[Justin A. Lemkul]

Yongchul Chung wrote:

Hello gmx-users,

I ran two short simulation in series (simulation A -- simulation B). 
The output *.gro file from the simulation A was used as an input file 
for the simulation B. If I compare the energy value at the end of 
simulation A, and t=0 at simulation B, they are different (0.1% 
deviation). However, if you supply checkpoint file, you get exactly the 
same value of the energy at t=0 for simulation B. I used gmxdump to 
check out the contents of cpt file. It seems like the file has some 
extra components compared to gro file (which has position, and velocity 
information). Several extra things I found that might be relevant were 
'energy_aver', 'energy_sum', and 'energy_n[0]'. It seems like gromacs 
somehow use these values internally to match the energy value at the 
start of simulation B to the end of simulation A. 

Can someone tell me why there's an error in the energy value if we don't 
supply the cpt file, but with cpt file, there's no error? I suspect it 
has to do with the extra information I mentioned above, but not sure 
where in the source code to look for more information. 



I can't provide any information on the specifics in the code, but if you think 
about the purpose and function of the .cpt file, it makes sense.  The .cpt file 
contains information about the entire state of the system, which is described by 
more than just position and velocities, which, in the .gro file, are in limited 
precision.


For a bit more:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation

-Justin


Thanks,

Greg

I'm appending the data, commands, and mdp file below for the reference.

// commands
1) Simulation A
grompp -f grompp.mdp -c input_to_A.gro -n index.ndx -p topol.top
mdrun -s topol.tpr -c output_of_A.gro

2-1) Simulation B (w/o checkpoint)
grompp -f grompp.mdp -c output_of_A.gro -n index.ndx -p topol.top
mdrun -s topol.tpr -c output_of_B.gro

2-2) Simulation B(w/ checkpoint)
grompp -f grompp.mdp -c output of A.gro -n index.ndx -p topol.top -t 
state.cpt

mdrun -s topol.tpr -c output_of_B_with_state.gro

// data
Simulation A energy data
time bond bond-nc
angles  dihedral 
LJ(SR) potential   
kinetic   total energy
0.00  29233.408203  43995.722656  45702.835938  51693.003906  
-144114.10937526510.859375  85977.609375  112488.468750
0.003000  29246.806641  44015.367188  45684.222656  51694.019531  
-144110.90625026529.50  85964.890625  112494.390625
0.006000  29247.708984  44022.949219  45585.886719  51695.375000  
-144107.5026444.421875  86054.156250  112498.578125
0.009000  29241.958984  44016.546875  45426.968750  51697.175781  
-144104.26562526278.390625  86218.25  112496.640625
0.012000  29235.324219  44005.812500  45257.687500  51699.402344  
-144101.03125026097.203125  86396.218750  112493.421875
0.015000  29231.802734  43999.378906  45130.50  51701.945312  
-144098.0025965.625000  86528.429688  112494.054688
0.018000  29231.041016  43994.878906  45067.519531  51704.746094  
-144094.39062525903.796875  86595.398438  112499.195312
0.021000  29227.580078  43988.855469  45058.753906  51707.007812  
-144091.46875025890.718750  86615.390625  112506.109375
0.024000  29213.531250  43979.210938  45072.437500  51708.511719  
-144088.96875025884.718750  86626.640625  112511.359375
0.027000  29182.050781  43970.894531  45074.558594  51708.472656  
-144086.5025849.468750  8.546875  112516.015625
0.03  29130.822266  43963.402344  45045.148438  51706.945312  
-144083.96875025762.343750  86753.906250  112516.25


Simulation B energy data (w/o checkpoint supply)
time bond bond-nc
angles  dihedral 
LJ(SR)  potential   
kinetic   total energy
0.00  29177.361328  43958.375000  45142.761719  51717.425781  
-144082.890625 25913.031250  86762.046875  112675.078125
0.003000  29105.240234  43942.156250  45086.699219  51714.648438  
-144080.843750 25767.906250  86901.765625  112669.671875
0.006000  29024.171875  43924.238281  45048.691406  51711.386719  
-144079.562500 25628.921875  87035.437500  112664.359375
0.009000  28946.726562  43907.777344  45057.507812  51707.562500  
-144078.187500 25541.375000  87120.882812  112662.257812
0.012000  28883.349609  43891.914062  45115.203125  51703.593750  
-144076.875000 25517.187500  87146.593750  112663.781250
0.015000  28838.960938  43876.933594  45194.253906  51698.367188  
-144075.921875 25532.578125  87133.734375  112666.312500
0.018000  28811.880859  43862.824219  45258.449219  51691.171875  
-144074.359375 

Re: [gmx-users] checkpoint file and *.gro -- energy calculation

[Yongchul Chung]

Thanks Justin for your prompt reply. I am aware of the link you provided,
but it seems they are rather hand-waving. It would be nice if I could be
directed to a source code of some sort.

Greg

On Sat, Nov 13, 2010 at 11:50 AM, Justin A. Lemkul jalem...@vt.edu wrote:



 Yongchul Chung wrote:

 Hello gmx-users,

 I ran two short simulation in series (simulation A -- simulation B). The
 output *.gro file from the simulation A was used as an input file for the
 simulation B. If I compare the energy value at the end of simulation A, and
 t=0 at simulation B, they are different (0.1% deviation). However, if you
 supply checkpoint file, you get exactly the same value of the energy at t=0
 for simulation B. I used gmxdump to check out the contents of cpt file. It
 seems like the file has some extra components compared to gro file (which
 has position, and velocity information). Several extra things I found that
 might be relevant were 'energy_aver', 'energy_sum', and 'energy_n[0]'. It
 seems like gromacs somehow use these values internally to match the energy
 value at the start of simulation B to the end of simulation A.
 Can someone tell me why there's an error in the energy value if we don't
 supply the cpt file, but with cpt file, there's no error? I suspect it has
 to do with the extra information I mentioned above, but not sure where in
 the source code to look for more information.


 I can't provide any information on the specifics in the code, but if you
 think about the purpose and function of the .cpt file, it makes sense.  The
 .cpt file contains information about the entire state of the system, which
 is described by more than just position and velocities, which, in the .gro
 file, are in limited precision.

 For a bit more:


 http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation

 -Justin


  Thanks,

 Greg

 I'm appending the data, commands, and mdp file below for the reference.

 // commands
 1) Simulation A
 grompp -f grompp.mdp -c input_to_A.gro -n index.ndx -p topol.top
 mdrun -s topol.tpr -c output_of_A.gro

 2-1) Simulation B (w/o checkpoint)
 grompp -f grompp.mdp -c output_of_A.gro -n index.ndx -p topol.top
 mdrun -s topol.tpr -c output_of_B.gro

 2-2) Simulation B(w/ checkpoint)
 grompp -f grompp.mdp -c output of A.gro -n index.ndx -p topol.top -t
 state.cpt
 mdrun -s topol.tpr -c output_of_B_with_state.gro

 // data
 Simulation A energy data
 time bond bond-nc
  angles  dihedral LJ(SR)
 potential   kinetic   total energy
0.00  29233.408203  43995.722656  45702.835938  51693.003906
  -144114.10937526510.859375  85977.609375  112488.468750
0.003000  29246.806641  44015.367188  45684.222656  51694.019531
  -144110.90625026529.50  85964.890625  112494.390625
0.006000  29247.708984  44022.949219  45585.886719  51695.375000
  -144107.5026444.421875  86054.156250  112498.578125
0.009000  29241.958984  44016.546875  45426.968750  51697.175781
  -144104.26562526278.390625  86218.25  112496.640625
0.012000  29235.324219  44005.812500  45257.687500  51699.402344
  -144101.03125026097.203125  86396.218750  112493.421875
0.015000  29231.802734  43999.378906  45130.50  51701.945312
  -144098.0025965.625000  86528.429688  112494.054688
0.018000  29231.041016  43994.878906  45067.519531  51704.746094
  -144094.39062525903.796875  86595.398438  112499.195312
0.021000  29227.580078  43988.855469  45058.753906  51707.007812
  -144091.46875025890.718750  86615.390625  112506.109375
0.024000  29213.531250  43979.210938  45072.437500  51708.511719
  -144088.96875025884.718750  86626.640625  112511.359375
0.027000  29182.050781  43970.894531  45074.558594  51708.472656
  -144086.5025849.468750  8.546875  112516.015625
0.03  29130.822266  43963.402344  45045.148438  51706.945312
  -144083.96875025762.343750  86753.906250  112516.25

 Simulation B energy data (w/o checkpoint supply)
 time bond bond-nc
  angles  dihedral LJ(SR)
  potential   kinetic   total energy
0.00  29177.361328  43958.375000  45142.761719  51717.425781
  -144082.890625 25913.031250  86762.046875  112675.078125
0.003000  29105.240234  43942.156250  45086.699219  51714.648438
  -144080.843750 25767.906250  86901.765625  112669.671875
0.006000  29024.171875  43924.238281  45048.691406  51711.386719
  -144079.562500 25628.921875  87035.437500  112664.359375
0.009000  28946.726562  43907.777344  45057.507812  51707.562500
  -144078.187500 25541.375000  87120.882812  112662.257812
0.012000  28883.349609  43891.914062  45115.203125  51703.593750
  -144076.875000 25517.187500  87146.593750  112663.781250
0.015000 

Re: [gmx-users] checkpoint file and *.gro -- energy calculation

[Yongchul Chung]

Forgot to mention that I am using gromacs 4.0.3 with N=19200

Greg

On Sat, Nov 13, 2010 at 12:06 PM, Yongchul Chung yxc...@case.edu wrote:

 Thanks Justin for your prompt reply. I am aware of the link you provided,
 but it seems they are rather hand-waving. It would be nice if I could be
 directed to a source code of some sort.

 Greg


 On Sat, Nov 13, 2010 at 11:50 AM, Justin A. Lemkul jalem...@vt.eduwrote:



 Yongchul Chung wrote:

 Hello gmx-users,

 I ran two short simulation in series (simulation A -- simulation B). The
 output *.gro file from the simulation A was used as an input file for the
 simulation B. If I compare the energy value at the end of simulation A, and
 t=0 at simulation B, they are different (0.1% deviation). However, if you
 supply checkpoint file, you get exactly the same value of the energy at t=0
 for simulation B. I used gmxdump to check out the contents of cpt file. It
 seems like the file has some extra components compared to gro file (which
 has position, and velocity information). Several extra things I found that
 might be relevant were 'energy_aver', 'energy_sum', and 'energy_n[0]'. It
 seems like gromacs somehow use these values internally to match the energy
 value at the start of simulation B to the end of simulation A.
 Can someone tell me why there's an error in the energy value if we don't
 supply the cpt file, but with cpt file, there's no error? I suspect it has
 to do with the extra information I mentioned above, but not sure where in
 the source code to look for more information.


 I can't provide any information on the specifics in the code, but if you
 think about the purpose and function of the .cpt file, it makes sense.  The
 .cpt file contains information about the entire state of the system, which
 is described by more than just position and velocities, which, in the .gro
 file, are in limited precision.

 For a bit more:


 http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation

 -Justin


  Thanks,

 Greg

 I'm appending the data, commands, and mdp file below for the reference.

 // commands
 1) Simulation A
 grompp -f grompp.mdp -c input_to_A.gro -n index.ndx -p topol.top
 mdrun -s topol.tpr -c output_of_A.gro

 2-1) Simulation B (w/o checkpoint)
 grompp -f grompp.mdp -c output_of_A.gro -n index.ndx -p topol.top
 mdrun -s topol.tpr -c output_of_B.gro

 2-2) Simulation B(w/ checkpoint)
 grompp -f grompp.mdp -c output of A.gro -n index.ndx -p topol.top -t
 state.cpt
 mdrun -s topol.tpr -c output_of_B_with_state.gro

 // data
 Simulation A energy data
 time bond bond-nc
  angles  dihedral LJ(SR)
 potential   kinetic   total energy
0.00  29233.408203  43995.722656  45702.835938  51693.003906
  -144114.10937526510.859375  85977.609375  112488.468750
0.003000  29246.806641  44015.367188  45684.222656  51694.019531
  -144110.90625026529.50  85964.890625  112494.390625
0.006000  29247.708984  44022.949219  45585.886719  51695.375000
  -144107.5026444.421875  86054.156250  112498.578125
0.009000  29241.958984  44016.546875  45426.968750  51697.175781
  -144104.26562526278.390625  86218.25  112496.640625
0.012000  29235.324219  44005.812500  45257.687500  51699.402344
  -144101.03125026097.203125  86396.218750  112493.421875
0.015000  29231.802734  43999.378906  45130.50  51701.945312
  -144098.0025965.625000  86528.429688  112494.054688
0.018000  29231.041016  43994.878906  45067.519531  51704.746094
  -144094.39062525903.796875  86595.398438  112499.195312
0.021000  29227.580078  43988.855469  45058.753906  51707.007812
  -144091.46875025890.718750  86615.390625  112506.109375
0.024000  29213.531250  43979.210938  45072.437500  51708.511719
  -144088.96875025884.718750  86626.640625  112511.359375
0.027000  29182.050781  43970.894531  45074.558594  51708.472656
  -144086.5025849.468750  8.546875  112516.015625
0.03  29130.822266  43963.402344  45045.148438  51706.945312
  -144083.96875025762.343750  86753.906250  112516.25

 Simulation B energy data (w/o checkpoint supply)
 time bond bond-nc
  angles  dihedral LJ(SR)
  potential   kinetic   total energy
0.00  29177.361328  43958.375000  45142.761719  51717.425781
  -144082.890625 25913.031250  86762.046875  112675.078125
0.003000  29105.240234  43942.156250  45086.699219  51714.648438
  -144080.843750 25767.906250  86901.765625  112669.671875
0.006000  29024.171875  43924.238281  45048.691406  51711.386719
  -144079.562500 25628.921875  87035.437500  112664.359375
0.009000  28946.726562  43907.777344  45057.507812  51707.562500
  -144078.187500 25541.375000  87120.882812  

Re: [gmx-users] checkpoint file and *.gro -- energy calculation

[Mark Abraham]

On 14/11/2010 4:06 AM, Yongchul Chung wrote:
Thanks Justin for your prompt reply. I am aware of the link you 
provided, but it seems they are rather hand-waving. It would be nice 
if I could be directed to a source code of some sort.


They're hand-waving by design of course - a normal user doesn't care 
about the details so long as they know how to make it work right.


src/gmxlib/checkpoint.c has the details (in 4.5 at least), which vary 
quite a bit with MD algorithm and GROMACS version.


Mark



Greg

On Sat, Nov 13, 2010 at 11:50 AM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




Yongchul Chung wrote:

Hello gmx-users,

I ran two short simulation in series (simulation A --
simulation B). The output *.gro file from the simulation A was
used as an input file for the simulation B. If I compare the
energy value at the end of simulation A, and t=0 at simulation
B, they are different (0.1% deviation). However, if you
supply checkpoint file, you get exactly the same value of the
energy at t=0 for simulation B. I used gmxdump to check out
the contents of cpt file. It seems like the file has some
extra components compared to gro file (which has position, and
velocity information). Several extra things I found that might
be relevant were 'energy_aver', 'energy_sum', and
'energy_n[0]'. It seems like gromacs somehow use these values
internally to match the energy value at the start of
simulation B to the end of simulation A.
Can someone tell me why there's an error in the energy value
if we don't supply the cpt file, but with cpt file, there's no
error? I suspect it has to do with the extra information I
mentioned above, but not sure where in the source code to look
for more information.


I can't provide any information on the specifics in the code, but
if you think about the purpose and function of the .cpt file, it
makes sense.  The .cpt file contains information about the entire
state of the system, which is described by more than just position
and velocities, which, in the .gro file, are in limited precision.

For a bit more:


http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation

-Justin


Thanks,

Greg

I'm appending the data, commands, and mdp file below for the
reference.

// commands
1) Simulation A
grompp -f grompp.mdp -c input_to_A.gro -n index.ndx -p topol.top
mdrun -s topol.tpr -c output_of_A.gro

2-1) Simulation B (w/o checkpoint)
grompp -f grompp.mdp -c output_of_A.gro -n index.ndx -p topol.top
mdrun -s topol.tpr -c output_of_B.gro

2-2) Simulation B(w/ checkpoint)
grompp -f grompp.mdp -c output of A.gro -n index.ndx -p
topol.top -t state.cpt
mdrun -s topol.tpr -c output_of_B_with_state.gro

// data
Simulation A energy data
time bond bond-nc
   angles  dihedral
LJ(SR) potential  
kinetic   total energy

   0.00  29233.408203  43995.722656  45702.835938
 51693.003906  -144114.10937526510.859375  85977.609375
 112488.468750
   0.003000  29246.806641  44015.367188  45684.222656
 51694.019531  -144110.90625026529.50  85964.890625
 112494.390625
   0.006000  29247.708984  44022.949219  45585.886719
 51695.375000  -144107.5026444.421875  86054.156250
 112498.578125
   0.009000  29241.958984  44016.546875  45426.968750
 51697.175781  -144104.26562526278.390625  86218.25
 112496.640625
   0.012000  29235.324219  44005.812500  45257.687500
 51699.402344  -144101.03125026097.203125  86396.218750
 112493.421875
   0.015000  29231.802734  43999.378906  45130.50
 51701.945312  -144098.0025965.625000  86528.429688
 112494.054688
   0.018000  29231.041016  43994.878906  45067.519531
 51704.746094  -144094.39062525903.796875  86595.398438
 112499.195312
   0.021000  29227.580078  43988.855469  45058.753906
 51707.007812  -144091.46875025890.718750  86615.390625
 112506.109375
   0.024000  29213.531250  43979.210938  45072.437500
 51708.511719  -144088.96875025884.718750  86626.640625
 112511.359375
   0.027000  29182.050781  43970.894531  45074.558594
 51708.472656  -144086.5025849.468750  8.546875
 112516.015625
   0.03  29130.822266  43963.402344  45045.148438
 51706.945312  -144083.96875025762.343750  

Re: [gmx-users] checkpoint file and *.gro -- energy calculation

[Yongchul Chung]

Thanks, Mark.

Greg

On Sat, Nov 13, 2010 at 12:35 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 14/11/2010 4:06 AM, Yongchul Chung wrote:

 Thanks Justin for your prompt reply. I am aware of the link you provided,
 but it seems they are rather hand-waving. It would be nice if I could be
 directed to a source code of some sort.


 They're hand-waving by design of course - a normal user doesn't care
 about the details so long as they know how to make it work right.

 src/gmxlib/checkpoint.c has the details (in 4.5 at least), which vary quite
 a bit with MD algorithm and GROMACS version.

 Mark



  Greg

  On Sat, Nov 13, 2010 at 11:50 AM, Justin A. Lemkul jalem...@vt.eduwrote:



 Yongchul Chung wrote:

 Hello gmx-users,

 I ran two short simulation in series (simulation A -- simulation B). The
 output *.gro file from the simulation A was used as an input file for the
 simulation B. If I compare the energy value at the end of simulation A, and
 t=0 at simulation B, they are different (0.1% deviation). However, if you
 supply checkpoint file, you get exactly the same value of the energy at t=0
 for simulation B. I used gmxdump to check out the contents of cpt file. It
 seems like the file has some extra components compared to gro file (which
 has position, and velocity information). Several extra things I found that
 might be relevant were 'energy_aver', 'energy_sum', and 'energy_n[0]'. It
 seems like gromacs somehow use these values internally to match the energy
 value at the start of simulation B to the end of simulation A.
 Can someone tell me why there's an error in the energy value if we don't
 supply the cpt file, but with cpt file, there's no error? I suspect it has
 to do with the extra information I mentioned above, but not sure where in
 the source code to look for more information.


  I can't provide any information on the specifics in the code, but if you
 think about the purpose and function of the .cpt file, it makes sense.  The
 .cpt file contains information about the entire state of the system, which
 is described by more than just position and velocities, which, in the .gro
 file, are in limited precision.

 For a bit more:


 http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation

 -Justin


  Thanks,

 Greg

 I'm appending the data, commands, and mdp file below for the reference.

 // commands
 1) Simulation A
 grompp -f grompp.mdp -c input_to_A.gro -n index.ndx -p topol.top
 mdrun -s topol.tpr -c output_of_A.gro

 2-1) Simulation B (w/o checkpoint)
 grompp -f grompp.mdp -c output_of_A.gro -n index.ndx -p topol.top
 mdrun -s topol.tpr -c output_of_B.gro

 2-2) Simulation B(w/ checkpoint)
 grompp -f grompp.mdp -c output of A.gro -n index.ndx -p topol.top -t
 state.cpt
 mdrun -s topol.tpr -c output_of_B_with_state.gro

 // data
 Simulation A energy data
 time bond bond-nc
  angles  dihedral LJ(SR)
 potential   kinetic   total energy
0.00  29233.408203  43995.722656  45702.835938  51693.003906
  -144114.10937526510.859375  85977.609375  112488.468750
0.003000  29246.806641  44015.367188  45684.222656  51694.019531
  -144110.90625026529.50  85964.890625  112494.390625
0.006000  29247.708984  44022.949219  45585.886719  51695.375000
  -144107.5026444.421875  86054.156250  112498.578125
0.009000  29241.958984  44016.546875  45426.968750  51697.175781
  -144104.26562526278.390625  86218.25  112496.640625
0.012000  29235.324219  44005.812500  45257.687500  51699.402344
  -144101.03125026097.203125  86396.218750  112493.421875
0.015000  29231.802734  43999.378906  45130.50  51701.945312
  -144098.0025965.625000  86528.429688  112494.054688
0.018000  29231.041016  43994.878906  45067.519531  51704.746094
  -144094.39062525903.796875  86595.398438  112499.195312
0.021000  29227.580078  43988.855469  45058.753906  51707.007812
  -144091.46875025890.718750  86615.390625  112506.109375
0.024000  29213.531250  43979.210938  45072.437500  51708.511719
  -144088.96875025884.718750  86626.640625  112511.359375
0.027000  29182.050781  43970.894531  45074.558594  51708.472656
  -144086.5025849.468750  8.546875  112516.015625
0.03  29130.822266  43963.402344  45045.148438  51706.945312
  -144083.96875025762.343750  86753.906250  112516.25

 Simulation B energy data (w/o checkpoint supply)
 time bond bond-nc
  angles  dihedral LJ(SR)
  potential   kinetic   total energy
0.00  29177.361328  43958.375000  45142.761719  51717.425781
  -144082.890625 25913.031250  86762.046875  112675.078125
0.003000  29105.240234  43942.156250  45086.699219  51714.648438
  -144080.843750 25767.906250