[gmx-users] relative binding free energy calculation Gromacs 5.0.5

Sun Jan 31 16:13:41 CET 2016

What do you mean by "instability"?  You also don't quite say what these values mean but I guess they are the estimates of the free energy per each window as computed by different methods(?).  These values come obviously from the (linear) electrostatic transformation so playing with softcore parameters won't make any difference.

If you are concerned by their magnitudes you can always introduce additional lambda points.  BTW, you may want to keep the mass-lambdas at their initial values (see mailing list archive for details).

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Stefania Evoli [stefania.evoli at kaust.edu.sa]
Sent: 31 January 2016 12:59
To: gmx-users at gromacs.org
Subject: [gmx-users] relative binding free energy calculation Gromacs 5.0.5

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.evoli at kaust.edu.sa

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