I see. And how can I fix this ? Using trjconv -timestep ? I just want to be sure ...<br><br>Thank you<br><br><br><div class="gmail_quote">On Fri, May 2, 2008 at 1:57 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;"><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<div><div></div><div class="Wj3C7c"><br>
"maria goranovic" <<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="Wj3C7c">
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 following<br>
method to continue my simulation trajectories:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
>From the minimized structure, I first run a short 2 ps (1000 step)<br>
</blockquote>
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 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 make a<br>
new out-1.tpr file based on a dummy .mdp file, which contains all the 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 1000x<br>
0.002 = 2 ps. This seems to be the source of the problem somehow, because<br>
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<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>> wrote:<br>
<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="Wj3C7c">
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 <<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>
> > > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
> > > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> > > Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
> > > posting!<br>
> > > Please don't post (un)subscribe requests to the list. Use the www<br>
> > > interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
> > > Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
> > ><br>
> > _______________________________________________<br>
> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> > Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
> > posting!<br>
> > Please don't post (un)subscribe requests to the list. Use the www<br>
> > interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
> > Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
> ><br>
> ><br>
><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>
</div></div><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>
<br>
-----------------------------------------------------<div class="Ih2E3d"><br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
</div></blockquote><div class="Ih2E3d">
<br>
<br>
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
</div></blockquote><div><div></div><div class="Wj3C7c">
<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>
-----------------------------------------------------<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen