[gmx-users] free energy calculation , grompp crash

[Da-Wei Li]

Dear users

I tried free energy calculation but grompp couldn't go through. It stops
after

*******************
Generated 2278 of the 2278 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2278 of the 2278 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning H bonds into constraints...
Coupling 1 copies of molecule type 'Protein'
*******************

The CPU usage is 100%.

I just add following into the mdp file:

***************
free_energy              = yes
init_lambda              = 0.0
delta_lambda             = 0
sc_alpha                 =0.5
sc-power                 =1.0
sc-sigma                 = 0.3
couple-moltype           = Protein
couple-lambda0           = vdw-q
couple-lambda1           = none
***************

Does anyone have some idea about this problem?  thanks.

Another question is whether I can switch off "two molecules" (such as
protein+ligand) in free energy calculation? I searched this list and got
that 4.0.7 did support this. how about 4.5.4?

dawei
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