[gmx-users] AGAIN: demixing REMD trajectories

[David van der Spoel]

madeleine.kittner at mpikg.mpg.de wrote:
>> madeleine.kittner at mpikg.mpg.de wrote:
>>> 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
>>>
>> did you read the help text in the perl script?
> 
> Yes, I did.
> 
>> # If your exchange was every N ps and you saved every M ps you can make
>> for
>> # the missing frames by setting extra to (N/M - 1). If N/M is not integer,
>> # you're out of luck and you will not be able to demux your trajectories
>> at all.
> 
> In my case N=5 ps and M=20 ps which means (N/M-1) is not an integer and I
> m unlucky. But I only need to know every 20 ps at which temperature each
> replica is simulated. Even if I produce a replica_index file that contains
> only the information each 20 ps, trjcat produces one trajout.xtc file
> which contains only the box parameter as posted above.

I would think it is reverse N=20 M = 5, so you have to set the number to 
3. You can test it by computing RMSD for the resulting trajectories and 
seeing whether these are continuous.

> 
>> --
>> David van der Spoel, Ph.D.
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> 
> 
> ---
> Madeleine Kittner, PhD student
> Department of Theory and Bio-Systems
> Max Planck Institute of Colloids and Interfaces
> Research Campus Golm
> 14424 Potsdam, Germany
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se