[gmx-users] AGAIN: demixing REMD trajectories

[madeleine.kittner at mpikg.mpg.de]

Hi gromacs users,

I worked a on my problem (see mail below) and got some new questions:

I did REMD using 50 replicas using gromacs version 3.3, while the data
were saved every 20 ps and exchanges were attempted every 5 ps. I used
demux.pl to generate replica_temp.xvg and replica_index.xvg. To get
continuous trajectories I used trjcat from version 3.3.1 (it's not
available in older versions)

trjcat -f traj*.xtc -demux replica_index.xvg

I solved the segmentation fault problem by compiling gromacs 3.3.1
differently. But now I'm stuck with the same problem as other people
before. trjcat produces only one output file trajout.xtc which contains
only the box parameters and looks like this:

 trajout.xtc frame 0:
   natoms=         0  step=         0  time=         0  prec=         0
   box (3x3):
      box[    0]={ 5.46920e+00,  0.00000e+00,  0.00000e+00}
      box[    1]={ 1.82296e+00,  5.15645e+00,  0.00000e+00}
      box[    2]={-1.82292e+00,  2.57794e+00,  4.46567e+00}
not available: x
trajout.xtc frame 1:
   natoms=         0  step=      5000  time=        20  prec=         0
   box (3x3):
      box[    0]={ 5.46920e+00,  0.00000e+00,  0.00000e+00}
      box[    1]={ 1.82296e+00,  5.15645e+00,  0.00000e+00}
      box[    2]={-1.82292e+00,  2.57794e+00,  4.46567e+00}
not available: x
trajout.xtc frame 2:
.... and so on.

Is the problem caused by the different time frames in the traj*.xtc files
and the replica_index.xvg file? Or is it caused by mixing up the different
gromacs versions? For other people using the demux.pl script seemed to
solve all the problems but it does not in my case.

Thanks for your help.
Cheers, Madeleine

> Hi gromacs users,
>
> I ran a REMD simulation of 2 peptides in water using 50 replicas. To check
> the consistency of the REMD system I want to check the structure
> distributions of each replica. For that I need to demultiplex the
> (temperature) trajectories. I attempt exchanges every 5ps and save data
> every 20 ps.
>
> I used the demux.pl script to generate replica_index.xvg and
> replica_temp.xvg which look fine. But if I try to generate continuous
> trajectories for each replica using
>
> trjcat -f traj*.xtc -demux replica_index.xvg
>
> I get...
>
> Read 50 sets of 17272 points, dt = 5
>
> Reading frame       0 time    0.000   Segmentation fault
>
> Is the problem caused by the fact that the number of time frames in the
> trajectories don't match the number of time frames in the replica index
> file?
> I read through the earlier postings on this subject, after using demux.pl
> everyone seemed satisfied. So, I guess it works somehow and I just do
> something wrong I can't figure out.
>
> Thanks for your help.
> Cheers,
> Madeleine
>
>


---

Madeleine Kittner, PhD student
Department of Theory and Bio-Systems
Max Planck Institute of Colloids and Interfaces
Research Campus Golm
14424 Potsdam, Germany