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

[Justin Lemkul]

On 9/7/14 2:37 AM, Lyna Luo wrote:
> Dear GMX experts,
>
> I can not figure out how to make g_wham readin data from my pdo file below, even though I tried different -b option and component selections. Please see the error message below. Thank you so much! -L
>
> # UMBRELLA 3.0
>
> # Component selection: 0 0 1
>
> # nSkip 1
>
> # Ref. Group TestAtom
>
> # Nr. of pull groups 1
>
> # Group 1 GR1 Umb. Pos. 0 Umb. Cons. 2.0
>
> #####
>
> 5054910 6.86778783227709e-01
>
> 5054920 7.12201410957491e-01
>
> 5054930 7.20695103841784e-01
>
> 5054940 7.10706445794138e-01
>
> 5054950 7.30693655979543e-01
>
> 5054960 7.33930839499955e-01
>
> 5054970 7.45784725425651e-01
>
> 5054980 7.66841219351832e-01
>
> 5054990 7.61835548305989e-01
>

I don't know if this is a consequence of the email or it's the actual format of 
the .pdo file, but there are skipped lines between everything that will cause 
incorrect interpretation of contents.  Though if there were really a problem, 
there should be a fatal error, so I'm not 100% sure if this is a problem.

>
>
> 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 tt.dat -bins 5 -temp 300 -tol 0.001 -auto
>
>
> Found 1 pdo files in tt.dat

A single .pdo file corresponds to a single window.  You can't build a reaction 
coordinate from a single sampling window, so basically everything after this 
point is total junk.

-Justin

>
> Automatic determination of boundaries from 1 pdo files...
>
> Using gunzig executable /bin/gunzip
>
> Opening test.pdo.gz ... [100%]
>
>
> Determined boundaries to 100000002004087734272.000000 and -100000002004087734272.000000
>
>
> Opening test.pdo.gz ... [100%]
>
> WARNING, no data points read from file test.pdo.gz (check -b option)
>
>

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

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

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