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