[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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