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On 21/11/2010 10:58 PM, Hsin-Lin Chiang wrote:
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<pre>Hi,
Today I use serach and find this topic.
I got confused.
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations</a>
According the page of "extending simulation", in GROMACS ver.4, the commend is:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
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So you've created a new .tpr with a longer simulation time (but
which incidentally has the state of the previous .tpr)...<br>
<br>
<blockquote cite="mid:20101121114650.M64434@phys.sinica.edu.tw"
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<pre>mdrun -s next.tpr -cpi previous.cpt
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... and told mdrun to use that longer time, and the current state in
the checkpoint file. This will work, so long as you are not
attempting to change the thermodynamic ensemble, or similar.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:20101121114650.M64434@phys.sinica.edu.tw"
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<pre>
I use this two lines to continue my simulation and get success.
But now I'm much worried my data is wrong since I didn't use -e edr and -t trr as in the first line above.
The way that tpbconv should -e -t files is written in the part ver. 3.3.3 and before.
My GROMACS version is 4.0.5.
Am I right to use lines above to do extending simulation?
Hsin-Lin
>
>
> ----- Original Message -----
> From: Yongchul Chung <a class="moz-txt-link-rfc2396E" href="mailto:yxc...@case.edu"><yxc...@case.edu></a>
> Date: Thursday, November 4, 2010 10:28
> Subject: [gmx-users] extending simulation without cpt file
> To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
>
> > Hello gmxers,
> >
> > I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but
> > erased cpt file. However, I need to extend the simulation from the end of
> > the trajectory file. I know this will not be binary identical as stated
> > here (<a moz-do-not-send="true" href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations" rel="nofollow">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations</a>).
> > I used following commands.
> >
> > tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr
> > mdrun -s topolnew.tpr
> >
> > When I do this and run the simulation, for some reason, the simulation
> > starts from t=0 instead of t=102000. it seems like gromacs is writing the
> > file without recognizing it that it should start the trajectory from 102000
> > ps. Is this a known bug? If so, is there a way around to solve this problem?
>
> You've extended the run time of the original simulation, and forced it to
> start from the state in the new .tpr, but that state came from the original
> .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the
> checkpoint.
>
> Your best chance of continuing will come from reconstructing the .mdp
> suitably (use gmxcheck to compare resulting .tpr files) and using grompp to
> create a .tpr using the most recent endpoint permitted by your .trr + .edr.
Actually, Justin's right. tpbconv needs -e -t files. It's been so long since I
used it, I'd forgotten :-)
Mark
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