Thank you Mark,<br><br>I'm running gromacs 4.0.3., so I don't know if I should submit a bugzilla.<br>Please Do you know another way to restart my MD run?<br><br>Thanks,<br>Carla<br><br><div class="gmail_quote">On Tue, May 11, 2010 at 1:00 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">On 11/05/2010 7:55 PM, Carla Jamous wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi everyone,<br>
<br>
please I encountered a problem of potential energy rising suddenly<br>
during my simulation.<br>
Someone advised me to take the previous conformation of my system,<br>
center it in the box, minimize it & then restart my MD simulation, by<br>
taking the previous velocities of this conformation.<br>
So I did the centering and the minimization.<br>
<br>
Usually, I used to do the following for my MD run.<br>
tpbconv -s .tpr -extend 6000 -o .tpr<br>
mdrun -v -s .tpr -cpi state_.cpt -cpo state_.cpt -o .trr -c .gro -x .xtc<br>
-e .edr -g .log<br>
<br>
However, this time I need to go from the minimized structure.<br>
So in order to get a .tpr file of my minimized structure (.gro), I<br>
created a .mdp file with gen_vel=no and did:<br>
<br>
grompp -f .mdp -c minimized.gro -p .top -o minimized.tpr<br>
<br>
After that, I tried the following:<br>
<br>
tpbconv -s minimized.tpr -extend 6000 -o .tpr<br>
mdrun -v -s .tpr -cpi state_.cpt -cpo state_.cpt -o .trr -c .gro -x .xtc<br>
-e .edr -g .log<br>
<br>
and got this error message:<br>
<br>
*WARNING: This run will generate roughly 3410368410012306432 Mb of data<br>
<br>
starting mdrun 'Protein in water'<br>
6 steps, 12.0 ps (continuing from step 27, 54.0 ps).<br>
</blockquote>
<br></div>
That looks like a bug. The run time from your .mdp+tpbconv is 12ps, but the .cpt is already past that and GROMACS is using integer arithmetic inappropriately to get a huge number of steps (thus large output volume estimate) but no actual steps occur.<br>
<br>
If you're running GROMACS 4.0.7, please submit a bugzilla.<br>
<br>
Mark<br><font color="#888888">
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