Dear Users, I performed MD simulation on a calcium binding protein with bound calcium starting from the crystal structure using gromos96 forcefield with explicit solvent with NVT ensembles. I performed energy minimization of calcium bound protein with water and following this position restraint molecular dynamics was performed. Subsequently, MD was performed on the system. In a less than 100 ps the calcium ion diffuse away from protein. However, in the experiment (NMR and X-ray)the protein is stable in calcium bound form.
What could be the reason for this? How can this problem be fixed? Thanks. Sunita -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
