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> <
> > > > 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> <
> > 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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