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: [email protected] [[email protected]] On Behalf
Of Justin A. Lemkul [[email protected]]
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
========================================
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