FW: [gmx-developers] Free Energy Calculation

Emanuel Birru Emanuel.Birru at monash.edu
Thu Sep 2 04:58:09 CEST 2010



I am doing a partition coefficient of solute between 1-Octanol and water using gromacs ffG53a6 force field. Actually I am trying to reproduce Garrido et al' s paper (J. Chem Theory Comput. 2009). The first thing I have done is to predict the Gibbs free energy of salvation of pentane (my solute) in 1-Octanol by thermodynamics integration method using 16 λ (lambda) values. It works well for λ =0. 0.05, 0.1, 0.2, 0.3, 0.4 and 0.5. The problem has stated at λ=0.6 and it is LINCS error which says as follows:

Fatal error:

Too many LINCS warnings (1001)

If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem

The atoms that make the problem are pentane atoms.


I have put the parameter file that I am using on this link http://hydra.pharm.monash.edu.au/md_project/production.txt


Before I run the production simulation I minimized the system well as exactly stated on the paper.


After I got the error I have tried to run it again by changing the time step and the soft core value i.e sc_alpha and run three jobs independently

1.       With 1fs time step and sc_alpha = 1.51

2.       With 2fs time step changing sc_alpha to 0.5 and

3.       With 1fs time step and 0.5 sc_alpha

The same problem happened for 2 and 3 but 1 works well, but the average dVpot/d λ is not what I expected, its >+7. I could not figure it out where exactly the problem is.


Thanks in advance for your advise.





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