[gmx-users] Free energy calculations

Daniel Santos simul at oninetspeed.pt
Mon Sep 27 18:36:14 CEST 2004

Dear all,

I am doing a Free Energy calculation of a molecule inside a lipid bilayer, without success. 

I am constraining the relative distance (z axis) between the centre of mass of a molecule (inside the lipid bilayer) and the centre of mass of the lipids that are in a certain neighbourhood of that molecule. 

The simulations start OK and after a random number of steps (can vary from tens to thousands of picoseconds) GROMACS stops and a core dump is generated. 

The system is equilibrated (before starting the free energy calculations) and all seams OK with the energies and other properties while doing the free energy calculation... The pullout.ppa and pull.pdo output files are generated with success.

Some details:

1) I generate the pull.ndx with:

make_ndx -f box.gro -o pull.ndx

and remove the extra index numbers (I keep only the lipid and teste molecule atom indexes).

2)My pull.ppa contains the following settings:

verbose                 = no
runtype                 = constraint
reftype                 = dynamic

reference_group         = PLA
group_1                 = PSO

constraint_direction    = 0.0 0.0 1.0
pulldim                 = N N Y
reflag                  = 1

r                       = 1.0
rc                      = 1.5

Any help will be appreciated. Thanks in advance.

Best regards,

Daniel dos Santos

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