[gmx-users] tpr-files.dat and pullf-files.dat

[Justin A. Lemkul]

Poojari, Chetan wrote:
> Hello Justin,
> 
> I had made mistake in creating the .dat files.  
> 
> I created just 5 windows between 0.2 to 5nm as i wanted to feel how things would work before setting up my system for umbrella sampling. And also to save up my computational time. 
> 
> So, After running the command:
> 
> g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
> 
> I get the below message. In the second line of the message it says "Reading 2 tpr and pullf files"...........and as it can seen below it reads all the .tpr files. But it doesn't say anything about reading the .xvg files.
> Please can I know what exactly its doing here.
> 

Neither do I, but that's why the source code is available :)

Presumably it's some sort of intermediate check.  It looks like the rest of the 
process completed.  The data are probably meaningless, though, so don't draw too 
much from it.  Without sufficient window overlap, you'll have a poor PMF curve 
with lots of discontinuities.  I suspect that five windows, spaced from 0.2 to 5 
nm, will not really indicate if you've done anything correctly or not.

-Justin

> 
> 
> Found 5 tpr and 5 pull force files in tpr-files.dat and pullf-files.dat, respectively
> Reading 2 tpr and pullf files
> Automatic determination of boundaries...
> Reading file 144.tpr, VERSION 4.0.7 (single precision)
> File 144.tpr, 1 groups, geometry "distance", dimensions [N N Y], (1 dimensions)
> 	grp 0) k = 1000.000  inittial distance = 0.601453
> Reading file 169.tpr, VERSION 4.0.7 (single precision)
> Reading file 300.tpr, VERSION 4.0.7 (single precision)
> Reading file 400.tpr, VERSION 4.0.7 (single precision)
> Reading file 500.tpr, VERSION 4.0.7 (single precision)
> 
> Determined boundaries to 0.462181 and 5.585278
> 
> Reading file 144.tpr, VERSION 4.0.7 (single precision)
> Reading file 169.tpr, VERSION 4.0.7 (single precision)
> Reading file 300.tpr, VERSION 4.0.7 (single precision)
> Reading file 400.tpr, VERSION 4.0.7 (single precision)
> Reading file 500.tpr, VERSION 4.0.7 (single precision)
> 
> Initialized rapid wham stuff.
> 	   1) Maximum change 5.326426e+00
> Switched to exact iteration in iteration 44
> Converged in 45 iterations. Final maximum change 6.37158e-07
> 
> 
> 
> Kind regards,
> chetan.
> 
> 
> 
> 
> 
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: 16 December 2010 20:49
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] tpr-files.dat and pullf-files.dat
> 
> Poojari, Chetan wrote:
>> Hi,
>>
>> I am doing data analysis of umbrella sampling tutorial. I have created 2 files :
>>
>> a) tpr-files.dat  (under this folder i got )
>> 144.tpr
>> 169.tpr
>> 300.tpr
>> 400.tpr
>> 500.tpr
>>
>>
>> b) pullf-files.dat
>>
>> pullf144.xvg
>> pullf169.xvg
>> pullf300.xvg
>> pullf400.xvg
>> pullf500.xvg
>>
>>
>> When i run this command:
>>
>> g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
>>
>>
>> I get the following error:
>>
>> Found 0 tpr and 0 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 0 tpr and pullf files.
>>
>> But both tpr-files.dat and pullf-files.dat contain all the .tpr and .xvg files·
>>
>>
>>
>> Please can someone suggest me how to go about this error message.
>>
> 
> The only thing I can think of is incompatible line endings (i.e., Windows).
> Otherwise, plain text input is rather straightforward.
> 
> -Justin
> 
>>
>> Kind regards,
>> chetan.
>>
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> 
> --
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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