[gmx-users] Lambda and simulation problem

Matteo De Chiara matnamo at gmail.com
Fri Jan 29 18:17:27 CET 2010

Hello everybody,

I performed 100 simulation using a lambda step of 0.01 using gromacs
4.0.5 and Amber forcefield, starting always from the same structure (
a crystal with the ligand), minimizing for 3000 step and then starting
the md simulation.

Here the row about the changing atom in my .itp file

15   amber99_48  1  M5P     S15    1  -0.7162    32.0600 amber99_43
-0.7294    16.0000

and this is the mdp file concerning the free energy calculation:

free_energy         = yes
sc_power            =  1.0
sc_alpha            =  0.5
sc_sigma            =  0.3
delta_lambda        =  0.0
init_lambda         =  0.50

I succesfully wrote the topology for the alchemical transformation and
in both end simulations ( with Lambda =0 and Lambda =1) I have no

For the intermediate steps( i.e. lambda=0.5) , however, I found that
the Jennard-Jones and the Coulomb interactions are drammatically

Actually, the S-O atom seems desappeared and the aminoacids in the
active site change their position in order to reach a good equilibrium
as if the S-O was not there ( there are charded atoms all around).
Moreover the changing atom moves around going crushing against the
other atoms sorrounding without apparent problems.

How could it be?
Can someone help me?

Thank you!


Ph.D. Student
Matteo De Chiara
Dept. of Molecular Biology, University of Siena

Via Fiorentina 1,
53100 Siena Italy

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