You probably fond the problem. trjcat expects 10 ps intervals
between frames. If it is not the case it complains.
On Fri, 2 May 2008 13:14:07 +0200
"maria goranovic" <[EMAIL PROTECTED]> wrote:
I have gmxchecked my individual trr files. They should contain 10 frames
each, but the output looks like:
#####################
Reading frame 10 time 10002.000
Timesteps at t=10000 don't match (10, 2)
Last frame 10 time 10002.000
Item #frames
Step 11
Time 11
Lambda 11
Coords 11
Velocities 11
Forces 0
Box 11
gcq#54: "I'm a Wishbone and I'm Breaking" (Pixies)
#####################
I think I have some idea of what the problem might be. I use the following
method to continue my simulation trajectories:
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:
tpbconv -f out-1.trr -s out-1.tpr -e out-1.edr -extend 100 -o out-2.tpr
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:
grompp -f dummy.mdp -c out-1.gro -p temp.top -o out-1.tpr
#######
integrator = md
tinit = 0
init_step = 1000
nsteps = 0
dt = 0.002
etc...
#######
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:
Timesteps at t=21702 don't match (2, 8)
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.
So there are no missing frames, but how do I fix the timestamps and so ?
Thanks a lot for reading the long email and helping out
-maria
On Fri, May 2, 2008 at 12:25 PM, Xavier Periole <[EMAIL PROTECTED]> wrote:
On Fri, 2 May 2008 12:01:37 +0200
"maria goranovic" <[EMAIL PROTECTED]> wrote:
> I used:
>
> trjcat -o out.trr -f *trr
>
It looks like you have missing frames in your xtc files ... that
happens sometimes when the simulation is stopped and restarted
from the trr file whereas the buffer of the xtc file is not emptied.
Did you gmxcheck the xtc files?
On Fri, May 2, 2008 at 11:42 AM, Mark Abraham <[EMAIL PROTECTED]>
> wrote:
>
> maria goranovic wrote:
> >
> > > Hi,
> > >
> > > After using gmxcheck on a merged trajectory, I get the following
> > error
> > > throughout the trajectory. What does this mean ?
> > >
> >
> > How did you merge the trajectory?
> >
> > Thank you for the help.
> > >
> > >
> > >
> > > .....
> > > Timesteps at t=21610 don't match (8, 10)
> > > Reading frame 50 time 21670.002 Timesteps at t=21700 don't
> > match
> > > (10, 2)
> > >
> > > Timesteps at t=21702 don't match (2, 8)
> > >
> > > Timesteps at t=21710 don't match (8, 10)
> > > Reading frame 60 time 21760.002 Timesteps at t=21800 don't
> > match
> > > (10, 2)
> > > ....
> > >
> > > and so on.
> > >
> > >
> > > --
> > > Maria G.
> > > Technical University of Denmark
> > > Copenhagen
> > >
> > >
> > >
> > ------------------------------------------------------------------------
> > >
> > > _______________________________________________
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>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole <http://md.chem.rug.nl/%7Eperiole>
-----------------------------------------------------
_______________________________________________
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--
Maria G.
Technical University of Denmark
Copenhagen
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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