[gmx-users] Applying restraint onto Sodium Atoms

Carlos Navarrro Retamal cnavarro at utalca.cl
Wed May 7 23:11:00 CEST 2014

Hi everyone,  
I’m trying to perform a MD simulations of a LEA (late embryogenesis abundant) protein on different solvents with different water contents.  Our protein doesn’t have a neutral charge, so we have to add also 6 sodiums ions. When we use a system with just a few water molecules (500 and even less), the sodium ions start to interact with the protein and this one starts to fold around the ions in by adopting and non-standar  conformation.
So basically, my question is: Is there a way to apply a force (restraint) onto this 6 ions in order to avoid any kind of strange interactions between our protein and the different sodium ions?
Hope someone can help me,
Have a nice day,

Carlos Navarro Retamal
Bioinformatic engineer
PhD student in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl

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