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