[gmx-users] FEP problem with lambda perturbation 1 to 0.95

Ragnarok sdf fabracht1 at gmail.com
Thu Aug 6 22:57:56 CEST 2009

I am performing FEP do obtain the dimerization of a protein in
membrane. The lambda intervals i am using are 0.05 for each window.
After that I rerun each lambda .trr perturbing the system (plus)0.05
and (minus)0.05 lambda value. Then with g-energy I obtain the deltaG
for each delta lambda.
Well, I have encountered a problem when trying to simulate the last
window (1.0 - 0.95 ). The simulation runs for a while and then dies.
The log file says
Step 2200  Warning: Pressure scaling more than 1%.

Program mdrun_lam, VERSION 4.0.5
Source code file: constr.c, line: 136

Fatal error:
Too many LINCS warnings (1602)
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

I would appreciate some light on the matter.
Thank you
Fabrício Bracht

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