[gmx-users] REMD

[David van der Spoel]

merc mertens wrote:
>>> remd.xvg was build like described above. output is only one trajectory,
>> containing only box information.
>>> additionally i tried:
>>>
>>> trjcat -f traj0.trr traj1.trr traj2.trr ... -o j0.xtc j1.xtc j2.xtc ...
>> -demux remd.xvg
>>> but from that i got only one trajectory as output, too (also only
>> containing box info).
>> How about the trr files? Are they written with the same frequency as 
>> what you have in the remd.xvg file? Otherwise I don't know what will 
>> happen...
>>
>> -- 
>> David.
> 
> when trying:  gmxdump -f traj0.trr | grep time
> 
> sample output is:
>    natoms=     14670  step=         0  time=         0  lambda=         0
>    natoms=     14670  step=       500  time=         1  lambda=         0
>    natoms=     14670  step=      1000  time=         2  lambda=         0
>    natoms=     14670  step=      1500  time=         3  lambda=         0
>    natoms=     14670  step=      2000  time=         4  lambda=         0
>    natoms=     14670  step=      2500  time=         5  lambda=         0
> ...
> 
> the "time" stamps correspond to the first column in remd.xvg used for trjcat. further, if *xtc is chosen as output in trjcat, for every single frame the *xtc file contains the line: "not available: x", where there surely is x in the single *trr files!
> 
> e.g.: gmxdump_d -f traj0.trr
> 
> traj0.trr frame 0:
>    natoms=     14670  step=         0  time=         0  lambda=         0
>    box (3x3):
>       box[    0]={ 8.48915e+00,  0.00000e+00,  0.00000e+00}
>       box[    1]={ 0.00000e+00,  4.99054e+00,  0.00000e+00}
>       box[    2]={ 0.00000e+00,  0.00000e+00,  3.49561e+00}
>    x (14670x3):
>       x[    0]={ 1.98230e+00,  2.07120e+00,  3.06491e+00}
>       x[    1]={ 1.93097e+00,  2.10502e+00,  3.14505e+00}
>       x[    2]={ 1.92314e+00,  2.07599e+00,  2.98319e+00}
> ...
> 
> for sure i am doing something wrong here, i just do not get what.
> i am puzzled, thanks for any help, merc
> 
have you run
gmxcheck -f file.trr ?

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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