Hi,
I have a protein complex system, Initially i have minimized and equilibrate my system for 0.5ns.
Then i want to slowly relax the side chain and back bone of my protein. i used all the restart files in my configuration file. In namd tutorial it's written that, if we used restart file so we don't need to mentioned cell vector basis again because restart file already have.
when i ran my configuration file without cell vector basis value it gives me the following error.
FATAL ERROR: PME requires periodic boundary conditions.
Then i also blocked PME with # sign and then it run very smoothly. now please tell it's fine or it can effect on my results?
I have attached my configuration file.
Periodic boundary conditions are initially set in the form of cell basis vectors and cell origin in input at the first calculation when you minimized your system. Then, NAMD reads that information from restart files in subsequent steps (equilibration and minimization)
PME regards the way in which you treat electrostatics. If you select this method to calculate electrostatic interactions in your periodic system, you had to include the proper specification in the input files to all your steps (minimization, equilibration and simulation). Just include in the input files these two lines:
PME yes
PMEGridSpacing 1.0
and in principle everything had to go fine (the second line lets NAMD detemine the grid for performing Particle Mesh Ewald calculations)
Periodic boundary conditions are initially set in the form of cell basis vectors and cell origin in input at the first calculation when you minimized your system. Then, NAMD reads that information from restart files in subsequent steps (equilibration and minimization)
PME regards the way in which you treat electrostatics. If you select this method to calculate electrostatic interactions in your periodic system, you had to include the proper specification in the input files to all your steps (minimization, equilibration and simulation). Just include in the input files these two lines:
PME yes
PMEGridSpacing 1.0
and in principle everything had to go fine (the second line lets NAMD detemine the grid for performing Particle Mesh Ewald calculations)
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