[gmx-users] extending simulation without cpt file

Hsin-Lin Chiang jiangsl at phys.sinica.edu.tw
Sun Nov 21 12:58:43 CET 2010


Today I use serach and find this topic.

I got confused.


According the page of "extending simulation", in GROMACS ver.4, the commend is:

tpbconv -s previous.tpr -extend timetoextendby -o next.tpr

mdrun -s next.tpr -cpi previous.cpt

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?




> ----- Original Message -----

> From: Yongchul Chung <yxc... at case.edu>

> Date: Thursday, November 4, 2010 10:28

> Subject: [gmx-users] extending simulation without cpt file

> To: Discussion list for GROMACS users <gmx-users at gromacs.org>


> > 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 (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations).

> > 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 :-)


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