[gmx-users] extending simulation without cpt file

[Mark Abraham]

----- Original Message -----
From: Hsin-Lin Chiang <jiangsl at phys.sinica.edu.tw>
Date: Monday, November 22, 2010 14:51
Subject: Re: [gmx-users] extending simulation without cpt file
To: gmx-users at gromacs.org

>  Hi, Mark
> 
> So, You mean I can get correct extending simulation without 
> using -e ede and -t trr in GROMACS ver.4.


Yes. That's what the link you gave says.


Mark

> Then I can set my mind at rest.
> 
> Thank you for your reply.
> 
> Hsin-Lin
> >>Hi, Today I use serach and find this topic.
> >>
> >>I got confused.
> >>
> >>
> >>
> >>http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
> >>
> >>According the page of "extending simulation", in GROMACS 
> ver.4, the commend is:
> >>
> >>
> >>
> >>tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> >So you've created a new .tpr with a longer simulation time (but which
> >incidentally has the state of the previous .tpr)...
> >
> >>mdrun -s next.tpr -cpi previous.cpt
> >... 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.
> >
> >Mark
> >
> >>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<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 :-)
> >>
> >>
> >>
> >>  Mark
> >>
> >>
> >>
> >>
> >>
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