[gmx-users] AGAIN: demixing REMD trajectories

[David van der Spoel]

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
> 
>> 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.
>>

did you read the help text in the perl script?

in the latest version (attached) there is an option for your situation.

>> 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
> 
> 
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: demux.pl
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080225/16abec93/attachment.pl>