Unreasonable umbrella potential plot

User discussions
1

GROMACS version: version 2021.5
GROMACS modification: Yes/No
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Hello Gromacs users,

I’m a beginner computational chemistry student using Gromcs for my undergraduate research. I capped a 3 nm Silver nanoparticle with amino acid ; ARG and carried out umbrella sampling by pulling one amino acid residue away from the nanoparticle. I followed the umbrella sampling tutorial designed by @jalemkul . However when I used wham, I get a quite odd looking plot for umbrella potential. Also I get 2 warnings : WARNING, no data point in bin 14 (z=0.510967) !
You may not get a reasonable profile. Check your histograms!

WARNING, no data point in bin 57 (z=1.64511) !
You may not get a reasonable profile. Check your histograms!

Here’s the histogram and the umbrella potential plot.

Histogram
Histogram995×759 9.19 KB

Umbrella potential
Umbrella potential1002×811 6.86 KB

If anyone could tell me where it has gone wrong or the possible reason for the unreasonable plot it would be of great help. Thank you in advance.

Regards,
Maleesha

2

try to reduce number of bins, with gmx wham -bins option. By default there is 200 bins, reduce it to lets say 50 first. But in general you need to simulate more umbrella windows. for example in you figures there is a gap between umbrella #5 and #6, which causes energy jump at ~1.65 nm in PMF, also there is definitely a problem with umbrella at ~3.6 nm.

3

My apologies for not responding soon. Thank you so much for your suggestions. I also found an error in my mdp file and I’m going to increse the number of sampling windows as you have suggested. Thank you for your kindness.

Maleesha.