Hello,
you'll need to check if you are properly sampling the different states
in your simulations, which should be possible by analyzing the
histograms you can get from gmx bar -oh
Otherwise you'll need to check if your simulation parameters are
realistic, as the program warns you :)
Cheers
Paul
On 13/02/2020 21:19, Sadaf Rani wrote:
Dear Gromacs users
I am doing free energy calculation of a ligand with protein. When I do gmx
bar it gives me the following error:-
Temperature: 298.15 K
Detailed results in kT (see help for explanation):
lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/-
0 13.29 0.061.28 0.101.37 0.081.54 0.09
1 21.41 0.040.47 0.050.31 0.050.77 0.03
2 30.88 0.060.09 0.020.06 0.010.41 0.06
3 40.67 0.03 -0.01 0.03 -0.01 0.030.25 0.01
4 50.50 0.010.11 0.000.10 0.000.22 0.01
5 60.33 0.01 -0.04 0.01 -0.07 0.030.21 0.03
6 70.27 0.020.07 0.040.04 0.020.22 0.03
7 80.11 0.030.05 0.020.04 0.010.16 0.01
8 90.11 0.01 -0.09 0.02 -0.10 0.020.17 0.01
9 100.08 0.020.12 0.010.12 0.010.20 0.00
10 11 -0.04 0.03 -0.01 0.03 -0.01 0.030.18 0.01
11 12 -0.09 0.030.06 0.030.05 0.030.19 0.02
12 13 -0.02 0.03 -0.12 0.03 -0.12 0.030.23 0.01
13 14 -0.01 0.030.17 0.030.16 0.030.28 0.02
14 15 -0.06 0.03 -0.09 0.03 -0.09 0.030.25 0.01
15 16 -0.04 0.030.13 0.040.13 0.040.29 0.01
16 17 -0.15 0.030.04 0.010.04 0.010.24 0.01
17 18 -0.14 0.030.01 0.020.01 0.020.25 0.01
18 19 -0.07 0.03 -0.01 0.01 -0.08 0.020.27 0.01
19 20 -0.05 0.010.18 0.000.09 0.000.28 0.00
WARNING: Some of these results violate the Second Law of Thermodynamics:
This is can be the result of severe undersampling, or (more likely)
there is something wrong with the simulations.
Final results in kJ/mol:
point 0 - 1, DG 8.14 +/- 0.14
point 1 - 2, DG 3.50 +/- 0.09
point 2 - 3, DG 2.19 +/- 0.14
point 3 - 4, DG 1.66 +/- 0.07
point 4 - 5, DG 1.24 +/- 0.02
point 5 - 6, DG 0.83 +/- 0.02
point 6 - 7, DG 0.66 +/- 0.06
point 7 - 8, DG 0.28 +/- 0.08
point 8 - 9, DG 0.28 +/- 0.03
point 9 - 10, DG 0.19 +/- 0.05
point 10 - 11, DG -0.10 +/- 0.08
point 11 - 12, DG -0.22 +/- 0.07
point 12 - 13, DG -0.05 +/- 0.08
point 13 - 14, DG -0.03 +/- 0.08
point 14 - 15, DG -0.16 +/- 0.07
point 15 - 16, DG -0.10 +/- 0.07
point 16 - 17, DG -0.37 +/- 0.07
point 17 - 18, DG -0.35 +/- 0.08
point 18 - 19, DG -0.17 +/- 0.06
point 19 - 20, DG -0.13 +/- 0.02
total 0 - 20, DG 17.29 +/- 0.47
I have read in the link that I should not have negative entropy values in
my simulation
https://www.mail-archive.com/gmx-users@gromacs.org/msg55772.html.
Can anyone please suggest me what could be wrong during my simulation and
how should I fix it?
Thank you
Sadaf Rani
Ph.D. visiting student
Lancaster University
Uk
--
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594
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