[gmx-users] GROMACS reproducibility

Lucio Ricardo Montero Valenzuela lucioric at ibt.unam.mx
Fri Apr 16 23:54:38 CEST 2010

Hi. I am modelling a putative interaction between two proteins by doing MD of
the docked complex with GROMACS 4.0. But each time I run the MD simulating 200
ps, the evolves in a different manner, and the average coordinates are
different in a loop believed to help to the interaction. When I plot the LJ and
coulumb energies between the two proteins, they are two different. ¿Is it
reasonable to select the simulation that gives the better energies and moves
the interaction loop towards the interaction partner, and continue with these
simulation for ~2 nanoseconds? ¿or I have to do further analysis?.
Sincerely yours.

Lucio Ricardo Montero Valenzuela
Estudiante de doctorado en Ciencias Bioquímicas
Lab. del Dr. Federico Sánchez
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad 2001, Col. Chamilpa
Cuernavaca 62210

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