[gmx-users] free energy calculation

Paolo Cerri Paolo.Cerri at mi.infn.it
Thu Jan 25 11:03:52 CET 2007

Dear all,

I'm trying to calculate free energy differences using the standard
method of thermodynamic integration.I calculate dG/dlambda for different
values of lambda and then integrate.

When decoupling LJ interactions i have LINCS WARNING:

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.007366 (between atoms 7 and 8) rms 0.002535
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      7      8   50.1    0.1010   0.1017      0.1010
      9     10   65.8    0.1090   0.1085      0.1090
     17     18   32.1    0.1010   0.1011      0.1010
     17     19   32.0    0.1010   0.1011      0.1010
and eventually the simulation stops (during the equlibration run at
lambda >= 0.9)

I obtain the following message:

Program mdrun, VERSION 3.3.1
Source code file: clincs.c, line: 559
Fatal error:
Too many LINCS warnings (10001) - aborting to avoid logfile runaway.
This normally happens when your system is not sufficiently
equilibrated,or if you are changing lambda too fast in free energy
simulations.If you know what you are doing you can adjust the lincs
warning threshold
in your mdp file, but normally it is better to fix the problem.

I remark that in my simulations lambda is not changed continuously
during simulation, but i perform several simulations at different fixed
lambda values.

I change only LJ interactions (having previusly turned of Coulomb
I use  Amber forcefield  ffamber99

thanks in advance


More information about the gromacs.org_gmx-users mailing list