I am doing umbrella sampling using Justin Gromacs tutorial for DNA ligand complex. I am not able to understand how to make tpr-files.dat and pullf-files.dat. I manually paste umbrella.tpr file and pullf.tpr file in .dat files nut the profile.xvg formed is empty.
Please let me know how to form .dat files in umbrella sampling for gmx wham command.
After umbrella simulations, for each window, you will have these files topol1.tpr, topol2.tpr, topol3.tpr, and so on. and also pullf1.xvg, pullf2.xvg, and so on.
Create two files, namely tpr-files.dat and pullf-files.dat.
Paste the name of tpr and xvg files serially (one file name in each line) in the above-mentioned files. And then run gmx wham. Make sure the tpr and files are in the same directory where you will run gmx wham.
Rahul Sahu I have done the same thing but the profile.xvg file form is empty.
Rahul Sahu gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
Pallavi Agrawal you did right.
Since gmx wham does not call other files than tpr and pull files, please check the pullf.xvg files, it is empty or not.
Rahul Sahu pullf.xvg is not empty. I have attached the relatable files here.
Their is a warning when gmx wham command is given-
WARNING, no data point in bin 182 (z=4.81008) !
You may not get a reasonable profile. Check your histograms!
Please check and suggest.
Thank you in advance
Pallavi Agrawal I am able to run gmx wham and its generates histogram and profile files.
The warning you are getting is because you have not mentioned all the tpr and pullf files in the dat file (I think), so that there are no data to fill those histograms.
try with less number of bins in -bins
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