Problem in umbrella sampling

[Pallavi]

GROMACS version:
GROMACS modification: Yes/No
Here post your question
I am doing umbrella sampling between dna and ligand and i generated 5 frames in conf.gro files.
with the wham command, gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -bins 50
I got multiple warning

Found 5 tpr and 5 pull force files in tpr-files.dat and pullf-files.dat, respectively
Reading 5 tpr and pullf files
Automatic determination of boundaries…
Reading file umbrella0.tpr, VERSION 2021.3 (single precision)

File umbrella0.tpr, 1 coordinates, with these options:
Geometry distance k = 1000 position = 1.16322 dimensions [N N Y] (1 dimensions). Used: Yes
Pull group coordinates of 0 groups expected in pullx files.
Reference value of the coordinate not expected in pullx files.
Use option -v to see this output for all input tpr files

Reading pull force file umbrella0_pullf.xvg, expecting 2 columns:
Columns for pull coordinate 1
reaction coordinate: 1
center-of-mass of groups: 0
reference position column: No
Found 100001 times in umbrella0_pullf.xvg
Reading file umbrella1.tpr, VERSION 2021.3 (single precision)
Reading file umbrella2.tpr, VERSION 2021.3 (single precision)
Reading file umbrella3.tpr, VERSION 2021.3 (single precision)
Reading file umbrella4.tpr, VERSION 2021.3 (single precision)

Determined boundaries to 0.972951 and 5.557482

Reading file umbrella0.tpr, VERSION 2021.3 (single precision)
Reading file umbrella1.tpr, VERSION 2021.3 (single precision)
Reading file umbrella2.tpr, VERSION 2021.3 (single precision)
Reading file umbrella3.tpr, VERSION 2021.3 (single precision)
Reading file umbrella4.tpr, VERSION 2021.3 (single precision)

Back Off! I just backed up histo.xvg to ./#histo.xvg.3#
Wrote histo.xvg
Getting initial potential by integration.

WARNING, no data point in bin 5 (z=1.47725) !
You may not get a reasonable profile. Check your histograms!

WARNING, no data point in bin 6 (z=1.56894) !
You may not get a reasonable profile. Check your histograms!

WARNING, no data point in bin 7 (z=1.66063) !
You may not get a reasonable profile. Check your histograms!

WARNING, no data point in bin 8 (z=1.75232) !
You may not get a reasonable profile. Check your histograms!

WARNING, no data point in bin 9 (z=1.84401) !
You may not get a reasonable profile. Check your histograms!

WARNING, no data point in bin 10 (z=1.9357) !
You may not get a reasonable profile. Check your histograms!

WARNING, no data point in bin 11 (z=2.02739) !
You may not get a reasonable profile. Check your histograms!

WARNING, no data point in bin 17 (z=2.57754) !
You may not get a reasonable profile. Check your histograms!

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[egmarklund]

You have insufficient (zero) sampling in some parts on your reaction coordinate. Have you checked the histograms (as gmx wham told you)?

[Pallavi]

Yes i have checked it. I will post it too. It gives 5 peaks of 5 different color at around 5000 counts.

Pallavi Agrawal
Research Scholar
BSBE
IIT Roorkee

[egmarklund]

The warnings suggest that the combined histograms have zero counts in several intervals between 1.47 and 2.58 nm. Your PMF also looks quite choppy, so it seems you need better statistics. Without having seen the histograms I would guess that the best solution is to add more simulations with umbrella potentials covering the parts of the reaction coordinate where the sampling is low. How well do the histograms overlap?

[Pallavi]

not overlapping

[egmarklund]

Well then you have a problem. The sampling in neighbouring umbrellas need to overlap, because they each just give a local view of the PMF. In order to piece everything together to a complete PMF across the reaction coordinate you need overlap so that the algorithm knows how the pieces fit together.

[Pallavi]

i am attaching both the files. i have not use setumbrellascript files as i have no idea how to use it. and it gave the coordinates of box and center of mass as default as given in the tutorial.
i have generated 5 frames and run it randomly and found this error.

[jalemkul]

@Pallavi

i have not use setumbrellascript files as i have no idea how to use it. and it gave the coordinates of box and center of mass as default as given in the tutorial.

Here’s your problem :)

First, don’t try to literally apply the tutorial to your system. The input settings, window spacing, and force constants needed are probably going to be different. It is readily apparent that your windows are nowhere near correctly constructed since there are huge gaps between the histograms. If you don’t know what you’re doing or how to use the various scripts and protocols, you probably won’t get a good result. Back up and reconsider your approach.

[Pallavi]

Thank you for your response.

Pallavi Agrawal
Research Scholar
BSBE
IIT Roorkee

[Pallavi]

i have calculated com and generate different .tpr files and pullf files. but the tpr-files.dat is not working. i have given the wham command
it said-

File input/output error:
umbrella0.tpr

tpr-files.dat (248 Bytes)
pullf-files.dat (350 Bytes)

all other files are working .gro, .log, .xvg

[jalemkul]

The error means umbrella0.tpr is not present in the working directory.

[Pallavi]

i have done umbrella sampling for DNA-ligand and get profile.xvg file and histo.xvg after 17 umbrella simulation with 0.2 nm difference. is the results i am attaching is useful or i have to do more simulations. please reply.
Thank you in advance.