Dear users,
I’m performing relative binding free energy calculation in Gromacs 5.0.5. In
the mdp files I’m using the following section
free-energy = yes
init_lambda_state = LAMBDA
fep_lambdas = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0
1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
vdw_lambdas = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6
0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0
;couple-moltype = LIG
;couple-lambda0 = vdw-q
;couple-lambda1 = none
;couple-intramol = no
sc-alpha = 0.5
sc-sigma = 0.3
sc-power = 1.0
sc-r-power = 6
sc-coul = no
nstdhdl = 100
calc-lambda-neighbors = -1
And I obtained the following values
0 -- 1 16.498 +- 0.147 16.458 +- 0.173 18.142 +- 0.465
13.644 +- 0.351 16.264 +- 0.411 16.264 +- 0.413
1 -- 2 7.086 +- 0.143 6.982 +- 0.159 10.223 +- 0.246
4.168 +- 0.299 6.971 +- 0.341 6.971 +- 0.454
2 -- 3 -1.954 +- 0.114 -1.685 +- 0.129 -1.043 +- 0.574
-3.884 +- 0.392 -1.883 +- 0.356 -1.883 +- 0.356
3 -- 4 -13.604 +- 0.139 -13.271 +- 0.145 -10.960 +- 0.574
-18.048 +- 0.234 -14.286 +- 0.601 -13.222 +- 0.167
4 -- 5 0.089 +- 0.003 0.093 +- 0.003 0.079 +- 0.005
0.099 +- 0.003 0.091 +- 0.003 0.085 +- 0.000
5 -- 6 0.078 +- 0.004 0.079 +- 0.004 0.094 +- 0.003
0.062 +- 0.008 0.087 +- 0.003 0.080 +- 0.000
6 -- 7 0.141 +- 0.008 0.130 +- 0.011 0.110 +- 0.017
0.170 +- 0.001 0.170 +- 0.001 0.143 +- 0.001
7 -- 8 0.123 +- 0.005 0.131 +- 0.006 0.155 +- 0.001
0.096 +- 0.011 0.154 +- 0.001 0.121 +- 0.001
8 -- 9 0.063 +- 0.005 0.063 +- 0.006 0.071 +- 0.011
0.056 +- 0.001 0.056 +- 0.001 0.095 +- 0.001
9 -- 10 0.012 +- 0.004 0.002 +- 0.005 0.028 +- 0.001
-0.004 +- 0.008 0.028 +- 0.001 0.065 +- 0.001
10 -- 11 0.019 +- 0.008 0.030 +- 0.011 -0.036 +- 0.009
0.084 +- 0.011 0.007 +- 0.007 0.027 +- 0.001
11 -- 12 0.016 +- 0.006 0.013 +- 0.007 0.019 +- 0.008
0.008 +- 0.009 0.018 +- 0.006 -0.004 +- 0.000
12 -- 13 0.012 +- 0.007 0.015 +- 0.008 -0.004 +- 0.010
0.028 +- 0.009 0.012 +- 0.007 -0.018 +- 0.000
13 -- 14 -0.011 +- 0.008 -0.010 +- 0.009 0.015 +- 0.011
-0.034 +- 0.010 -0.011 +- 0.008 -0.034 +- 0.000
14 -- 15 -0.049 +- 0.006 -0.049 +- 0.007 -0.055 +- 0.014
-0.044 +- 0.001 -0.044 +- 0.001 -0.054 +- 0.000
15 -- 16 -0.085 +- 0.003 -0.086 +- 0.004 -0.065 +- 0.001
-0.104 +- 0.005 -0.066 +- 0.001 -0.078 +- 0.001
16 -- 17 -0.116 +- 0.009 -0.116 +- 0.010 -0.132 +- 0.006
-0.100 +- 0.016 -0.129 +- 0.006 -0.109 +- 0.001
17 -- 18 -0.150 +- 0.009 -0.145 +- 0.010 -0.129 +- 0.018
-0.159 +- 0.001 -0.159 +- 0.001 -0.151 +- 0.001
18 -- 19 -0.218 +- 0.005 -0.220 +- 0.005 -0.219 +- 0.002
-0.218 +- 0.008 -0.219 +- 0.002 -0.211 +- 0.001
It is clear the instability of the first four lambda values. Can someone
suggest me a way to avoid it? I’m trying to use different sc-alpha, sc-power
and sc-r-power. Any suggestion?
Thank you,
Stefania
—
Dr. Stefania Evoli
Post-Doctoral Fellow
King Abdullah University of Science and Technology
Catalysis center - Bldg. 3, 4th floor, 4231–WS18
Thuwal, Kingdom of Saudi Arabia
stefania.ev...@kaust.edu.sa
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