[gmx-users] distance restraint

Paula Andrea Delgado Pinzon pa-delga at uniandes.edu.co
Thu Sep 27 18:04:48 CEST 2012

Hello gromacs users,

I am doing energy minimization of a big protein with distance restraint (i need to create interactions between a group of residues, so i need them to be close), but in the resultant pdb a don't see those residues close, so how can I verify that the distance restraint are working?. Another unrelated question, is that i am doing the simulation in vacumm, also in this case i need to neutralized the system?, because with the command genion i need solvent to replace by ions, so in this case i can't do that part.

Thanks for your help


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