[gmx-users] AGAIN: demixing REMD trajectories

[madeleine.kittner at mpikg.mpg.de]

> 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.

>
> --
> 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