[gmx-users] timesteps don't match error
Xavier Periole
X.Periole at rug.nl
Fri May 2 17:21:44 CEST 2008
On Fri, 2 May 2008 17:06:08 +0200
"maria goranovic" <mariagoranovic at gmail.com> 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 <X.Periole at rug.nl> 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" <mariagoranovic at gmail.com> 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 <X.Periole at rug.nl>
>> > wrote:
>> >
>> > On Fri, 2 May 2008 12:01:37 +0200
>> > > "maria goranovic" <mariagoranovic at gmail.com> 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 <
>> > > Mark.Abraham at anu.edu.au>
>> > > > 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 gmx-users at gromacs.org
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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>
>> -----------------------------------------------------
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
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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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