Yes, I am quite sure I am not missing frames.<br><br>Do you mean "8 and 10 ARE the different time intervals it found not matching." <br><br>Thank you, again ! <br><br>-MAria<br><br><div class="gmail_quote">On Fri, May 2, 2008 at 5:21 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;">On Fri, 2 May 2008 17:06:08 +0200<div class="Ih2E3d"><br>
"maria goranovic" <<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>> wrote:<br>
</div><div class="Ih2E3d"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I see. And how can I fix this ? Using trjconv -timestep ? I just want to be<br>
sure ...<br>
</blockquote></div>
Well if you are missing frames it is difficult to fix it! But using -timestep<br>
indeed allows you to change it. Just make sure this is only a due to<br>
starting time and not something else. This would matter if you look<br>
at time dependent stuff ...<div class="Ih2E3d"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Timesteps at t=21610 don't match (8, 10)<br>
</blockquote></blockquote></div>
8 and 10 and the different time intervals it found not matching.<div><div></div><div class="Wj3C7c"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Reading frame 50 time 21670.002 Timesteps at t=21700 don't match (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 (10, 2)<br>
</blockquote>
<br>
<br>
On Fri, May 2, 2008 at 1:57 PM, Xavier Periole <<a href="mailto:X.Periole@rug.nl" target="_blank">X.Periole@rug.nl</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
You probably fond the problem. trjcat expects 10 ps intervals<br>
between frames. If it is not the case it complains.<br>
On Fri, 2 May 2008 13:14:07 +0200<br>
<br>
"maria goranovic" <<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>> wrote:<br>
<br>
> I have gmxchecked my individual trr files. They should contain 10 frames<br>
> 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<br>
> following<br>
> method to continue my simulation trajectories:<br>
><br>
> From the minimized structure, I first run a short 2 ps (1000 step)<br>
> ><br>
> simulation where I assign initial velocities. I obtain out-1.trr and<br>
> out-1.edr and out-1.gro. I then want to use tpbconv to continue the<br>
> 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<br>
> new<br>
> velocities would be assigned, and I might want to change some parameter<br>
> (like removing restraints) when I continue the simulation. So, I then<br>
> make a<br>
> new out-1.tpr file based on a dummy .mdp file, which contains all the<br>
> new<br>
> 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<br>
> 1000x<br>
> 0.002 = 2 ps. This seems to be the source of the problem somehow,<br>
> because<br>
> the error when I use gmxcheck on the merger trajectory is typically<br>
> 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<br>
> clear<br>
> to me. What does (2,8) mean ? I hope this makes things a little more<br>
> 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>
> On Fri, May 2, 2008 at 12:25 PM, Xavier Periole <<a href="mailto:X.Periole@rug.nl" target="_blank">X.Periole@rug.nl</a>><br>
> wrote:<br>
><br>
> 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>
> ><br>
> > > I used:<br>
> > ><br>
> > > trjcat -o out.trr -f *trr<br>
> > ><br>
> > 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?<br>
> ><br>
> > On Fri, May 2, 2008 at 11:42 AM, Mark Abraham <<br>
> > <a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
> > > wrote:<br>
> > ><br>
> > > maria goranovic wrote:<br>
> > > ><br>
> > > > > Hi,<br>
> > > > ><br>
> > > > > After using gmxcheck on a merged trajectory, I get the following<br>
> > > > 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<br>
> > > > 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<br>
> > > > 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>
> > ------------------------------------------------------------------------<br>
> > > > ><br>
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> > ><br>
> > ><br>
> > > --<br>
> > > Maria G.<br>
> > > Technical University of Denmark<br>
> > > Copenhagen<br>
> > ><br>
> ><br>
> > -----------------------------------------------------<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> <<a href="http://md.chem.rug.nl/%7Eperiole" target="_blank">http://md.chem.rug.nl/%7Eperiole</a>> <<br>
> > <a href="http://md.chem.rug.nl/%7Eperiole" target="_blank">http://md.chem.rug.nl/%7Eperiole</a>><br>
> ><br>
> > -----------------------------------------------------<br>
> > _______________________________________________<br>
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><br>
><br>
> --<br>
> Maria G.<br>
> Technical University of Denmark<br>
> Copenhagen<br>
><br>
<br>
-----------------------------------------------------<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> <<a href="http://md.chem.rug.nl/%7Eperiole" target="_blank">http://md.chem.rug.nl/%7Eperiole</a>><br>
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<br>
</blockquote>
<br>
<br>
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
</blockquote>
<br>
-----------------------------------------------------<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><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen