[gmx-users] Re: [gmx-developers] Free Energy Calculation

Sander Pronk pronk at cbr.su.se
Thu Sep 2 09:11:05 CEST 2010

It sounds like there is something wrong with the 'B' topology. Have you tried the 'decoupling' .mdp parameters? They're there specifically for your type of calculations.


On Sep 2, 2010, at 04:58 , Emanuel Birru wrote:

> Hi,
> 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.
> Cheers,
> Emanuel
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