[gmx-users] timesteps don't match error

[maria goranovic]

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
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