[gmx-users] Free Energy Calculations

jorge_quintero at ciencias.uis.edu.co jorge_quintero at ciencias.uis.edu.co
Mon Mar 8 02:46:24 CET 2010

Hello everybody

I tried to work with gromacs employing free energy calculations in a
dimeric protein system. First of all, doing a energy minimization a later
to compute the binding energy.  For all the cases, I use amber 94 FF.
However, I have two questions.

1.  When I made the energy minimization I got the following message:

WARNING 1 [file topol_B.itp, line 10531]:
  Some parameters for bonded interaction involving perturbed atoms are
  specified explicitly in state A, but not B - copying A to B

Although I could run that simulation.  But, is this right to my simulation?

2.  Is possible to use free energy methode (lambda, init_lambda, etc) to
calculate only binding energy between the system told at the beginning?. 
I guess is possible typing zero for temperature.  doesn't it?

I appreciate your support!

Jorge R. Quintero
Universidad Industrial de Santander
Bucaramanga, Santander - Colombia

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