I have gmxchecked my individual trr files. They should contain 10 frames each, but the output looks like:<br><br>#####################<br>Reading frame 10 time 10002.000 <br>Timesteps at t=10000 don't match (10, 2)<br>
Last frame 10 time 10002.000 <br><br><br>Item #frames<br>Step 11<br>Time 11<br>Lambda 11<br>Coords 11<br>Velocities 11<br>Forces 0<br>Box 11<br>
<br>gcq#54: "I'm a Wishbone and I'm Breaking" (Pixies)<br>#####################<br><br>I think I have some idea of what the problem might be. I use the following method to continue my simulation trajectories:<br>
<br>From the minimized structure, I first run a short 2 ps (1000 step) simulation where I assign initial velocities. I obtain out-1.trr and out-1.edr and out-1.gro. I then want to use tpbconv to continue the simulation, like so:<br>
<br>tpbconv -f out-1.trr -s out-1.tpr -e out-1.edr -extend 100 -o out-2.tpr<br><br>However, out-1.tpr cannot be used to continue the simulation, because new velocities would be assigned, and I might want to change some parameter (like removing restraints) when I continue the simulation. So, I then make a new out-1.tpr file based on a dummy .mdp file, which contains all the new parameters for the continuation run, and which looks like:<br>
<br>grompp -f dummy.mdp -c out-1.gro -p temp.top -o out-1.tpr<br><br>#######<br>integrator = md<br>tinit = 0<br>init_step = 1000<br>nsteps = 0<br>dt = 0.002<br>
<br>etc...<br>#######<br><br>So, the new tpr file suggests that the simulation should start from 1000x 0.002 = 2 ps. This seems to be the source of the problem somehow, because the error when I use gmxcheck on the merger trajectory is typically like:<br>
<br>Timesteps at t=21702 don't match (2, 8)<br><br>So, there seems to be a 2 ps offset. the above output is also not very clear to me. What does (2,8) mean ? I hope this makes things a little more clearer. <br><br>So there are no missing frames, but how do I fix the timestamps and so ?<br>
<br>Thanks a lot for reading the long email and helping out<br><br>-maria<br><br><br><br><br><br><br><br><div class="gmail_quote">On Fri, May 2, 2008 at 12:25 PM, Xavier Periole <<a href="mailto:X.Periole@rug.nl">X.Periole@rug.nl</a>> 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="Ih2E3d">On Fri, 2 May 2008 12:01:37 +0200<br>
"maria goranovic" <<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I used:<br>
<br>
trjcat -o out.trr -f *trr<br>
</blockquote></div>
It looks like you have missing frames in your xtc files ... that<br>
happens sometimes when the simulation is stopped and restarted<br>
from the trr file whereas the buffer of the xtc file is not emptied.<br>
<br>
Did you gmxcheck the xtc files?<div><div></div><div class="Wj3C7c"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
On Fri, May 2, 2008 at 11:42 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
maria goranovic wrote:<br>
<br>
> Hi,<br>
><br>
> After using gmxcheck on a merged trajectory, I get the following error<br>
> throughout the trajectory. What does this mean ?<br>
><br>
<br>
How did you merge the trajectory?<br>
<br>
Thank you for the help.<br>
><br>
><br>
><br>
> .....<br>
> Timesteps at t=21610 don't match (8, 10)<br>
> Reading frame 50 time 21670.002 Timesteps at t=21700 don't match<br>
> (10, 2)<br>
><br>
> Timesteps at t=21702 don't match (2, 8)<br>
><br>
> Timesteps at t=21710 don't match (8, 10)<br>
> Reading frame 60 time 21760.002 Timesteps at t=21800 don't match<br>
> (10, 2)<br>
> ....<br>
><br>
> and so on.<br>
><br>
><br>
> --<br>
> Maria G.<br>
> Technical University of Denmark<br>
> Copenhagen<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
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</blockquote>
<br>
<br>
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
</blockquote>
<br></div></div>
-----------------------------------------------------<br>
XAvier Periole - PhD<br>
<br>
NMR & Molecular Dynamics Group<br>
University of Groningen<br>
The Netherlands<br>
<a href="http://md.chem.rug.nl/%7Eperiole" target="_blank">http://md.chem.rug.nl/~periole</a><div><div></div><div class="Wj3C7c"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen