[gmx-users] no data read from file pdo.gz

[Justin Lemkul]

On 9/8/14 12:36 AM, Lyna Luo wrote:
> Hi Justin,
>
> The blank between lines are just from email format. I used only one window to see if g_wham can readin my data, but I actually have 64 window. Please see the error message below. Thanks again! -Lyna
>
>
> GROMACS:      gmx wham, VERSION 5.0
>
> Executable:   /usr/local/gromacs/bin/gmx
>
> Library dir:  /usr/local/gromacs/share/gromacs/top
>
> Command line:
>
>    g_wham -ip pdo.dat -bins 400 -temp 300 -tol 0.00001 -auto
>
>
> Found 64 pdo files in pdo.dat
>
> Automatic determination of boundaries from 64 pdo files...
>
> Using gunzig executable /bin/gunzip
>
> Opening disa_job13_pdo/job.job13.63.sort.colvars.traj,temp.bb.pdo.gz ... [100%]
>
>
> Determined boundaries to 100000002004087734272.000000 and -100000002004087734272.000000
>
>
> Opening disa_job13_pdo/job.job13.0.sort.colvars.traj,temp.bb.pdo.gz ... [ 2%]
>
> WARNING, no data points read from file disa_job13_pdo/job.job13.0.sort.colvars.traj,temp.bb.pdo.gz (check -b option)
>
> Opening disa_job13_pdo/job.job13.1.sort.colvars.traj,temp.bb.pdo.gz ... [ 3%]
>
> WARNING, no data points read from file disa_job13_pdo/job.job13.1.sort.colvars.traj,temp.bb.pdo.gz (check -b option)
>
> Opening disa_job13_pdo/job.job13.2.sort.colvars.traj,temp.bb.pdo.gz ... [ 5%]
>
> WARNING, no data points read from file disa_job13_pdo/job.job13.2.sort.colvars.traj,temp.bb.pdo.gz (check -b option)
>
>
> My pdo file looks like below. Is there something wrong with "component selection" or "nskip" or the two column data format?
>
> # UMBRELLA 3.0
>
> # Component selection: 0 0 1
>
> # nSkip 1
>
> # Ref. Group TestAtom
>
> # Nr. of pull groups 1
>
> # Group 1 GR1 Umb. Pos. 57.6 Umb. Cons. 2.0
>
> #####
>
> 5054910 5.76202567601903e+01
>
> 5054920 5.76153109776819e+01
>
> 5054930 5.76057280906502e+01
>
> 5054940 5.76000707360825e+01
>
> 5054950 5.75956747536078e+01
>
> 5054960 5.75863624004517e+01
>
> 5054970 5.75807826101227e+01
>
> 5054980 5.75752353578918e+01
>
> 5054990 5.75700050629966e+01
>
> 5055000 5.75644906348954e+01
>
> 5055010 5.75599694771144e+01
>
> 5055020 5.75577873701180e+01
>
> 5055030 5.75528304157033e+01
>

Any number of things could be wrong here.  Realize that .pdo files have been 
obsolete since about 2008, so the code referring to them is not routinely used 
or maintained.  So something could be going on there, and I suspect that is at 
least part of the problem, given the fact that the maximum and minimum can't be 
calculated properly.  Another possibility is that the contents of the files are 
misinterpreted; a quick look at the code suggests that the first field should be 
float (time in ps, not timestep) so something may be off.

You may want to consider using Alan Grossfield's WHAM program so you don't have 
to deal with all this .pdo-specific stuff; most people use that program for 
analyzing NAMD output.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================