On Fri, 2 May 2008 17:06:08 +0200
"maria goranovic" <[EMAIL PROTECTED]> wrote:
I see. And how can I fix this ? Using trjconv -timestep ? I just want to be
sure ...
Well if you are missing frames it is difficult to fix it! But using -timestep
indeed allows you to change it. Just make sure this is only a due to
starting time and not something else. This would matter if you look
at time dependent stuff ...
Timesteps at t=21610 don't match (8, 10)
8 and 10 and the different time intervals it found not matching.
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)
On Fri, May 2, 2008 at 1:57 PM, Xavier Periole <[EMAIL PROTECTED]> wrote:
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> <
> > http://md.chem.rug.nl/%7Eperiole>
> >
> > -----------------------------------------------------
> > _______________________________________________
> > gmx-users mailing list [email protected]
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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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