[gmx-users] Further discussion: the -extend function of the tpbconv command

Acoot Brett acootbrett at yahoo.com
Thu Apr 5 05:58:34 CEST 2012

Dear All,
According to "http://www.gromacs.org/Documentation/How-tos/Extending_Simulations" , the commands for extending MD are:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt

But if you read "http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File", it suggest for extension of MD, state.cpt should be used. But if we use state.cpt for extension, in

tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt

the "previous" in previous.tpr in tpbconv will be conflicting with "previous" in previous.cpt in mdrun.

In addition in command
trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact

can we change md_0_1.xtc to traj.xtc?

I am looking forward to getting a clarification from you.




 From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Wednesday, 4 April 2012 6:56 PM
Subject: Re: [gmx-users] the -extend function of the tpbconv command

On 4/04/2012 6:24 PM, Acoot Brett wrote: 
Hi Justin and All, 
>The on-line document on "Extending Simulations" writes, 
>"You might want to use the -append option of mdrun to append the new output to the old files. Note that this will only work when the old output files have not been modified by the user. Appending is the default behavior as of version 4.5." 
>We can see "Appending is the default behavior as of version 4.5", and what I use is version 4.5. Thus for mdrun, even without mention "-append " appending should be automatically done. 
>In addition, after the old output files were created, I only use the "trjconv" to process them, and I did not modify them.        
Any change is enough to prevent appending. mdrun computed a checksum
    when it wrote them, saved the checksums in the checkpoint file, and
    demands that newly-computed ones match when attempting to append
    later. Use only the original trajectory files when attempting to


>Thus the reason why the extended part output files were not automatically appended to my original old outputfiles according to what I have done (tpbconv -s previous.tpr -extend timetoextendby -o next.tpr       mdrun -s next.tpr -cpi previous.cpt) is still unclear. 
>Will you please give an explaination? 
>From: Justin A. Lemkul <jalemkul at vt.edu>
>To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
>Sent: Wednesday, 4 April 2012 10:36 AM
>Subject: Re: [gmx-users] the -extend function of the tpbconv command
>Acoot Brett wrote:
>> Dear All,
>>  I have completed a 1ns production MD. Then I
                      intended to extend it for another 1 ns.
>>  I use command
>>  "tpbconv -s previous.tpr -extend
                      timetoextendby -o next.tpr
>> mdrun -s next.tpr -cpi previous.cpt"
>>  I think the results will be automatically
                      attended to previous md_0_1.tpr and
>Only if you then run mdrun -append and the files
                      are appended.  tpbconv doesn't do any of this for
                      you, it just creates a new run input file capable
                      of running a longer simulation.  The fact that you
                      have a file called "md_0_1_noPBC.xtc" seems like
                      you've manipulated it in some way, so you
                      shouldn't (and likely can't) append to it.  You
                      should append to your original files.
>> Then I use "g_rms -s md_0_1.tpr -f
                      md_0_1_noPBC.xtc -o rmsd.xvg -tu ns" to get the
                      rmsd.xvg file. Then I use "xmgrace -nxy
                      potential.xvg" to display it. However I find for
                      the  curve the x-axis is from 0 ns to 1 ns, not
                      from 0 ns to 2 ns.
>If you haven't run a new simulation, you'll only
                      have the data that already exists.
>> The definition of "-extend" of the command
                      "tpbconv" is "Extend runtime by this amount (ps)".
                      Thus the commands I used are correct.
>You haven't shown us your actual tpbconv command,
                      so there's no way to verify that.  In any case,
                      tpbconv doesn't actually extend the simulation,
                      mdrun does.
>> Will you please tell me how to process for
                      the extension MD so that the curve of the rmsd.xvg
                      (and all the other xvg files) will have x-axis
                      from the 0 to the 2 ns (2 ns is the total MD time,
                      including the 1 ns extended part)?
>There are two steps here:
>You need to do both.
>-- ========================================
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
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