[gmx-users] timesteps don't match error
Xavier Periole
X.Periole at rug.nl
Fri May 2 13:57:29 CEST 2008
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>
>>
>> -----------------------------------------------------
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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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