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--- howto:biochem_qmmm [2017/07/25 11:11] – dvanrompaey
+++ howto:biochem_qmmm [2017/08/02 07:06] – dvanrompaey
@@ Line 69: / Line 69: @@
 Visualize your simulation to check for any abnormalities. Take a look at the output file, paying extra attention to any warnings you might receive. Note: CP2K will warn you about missing forcefield terms. You can have CP2K output these using ''[[inp>FORCE_EVAL/MM/PRINT/FF_INFO]]''.In this case, the missing terms are Urey-Bradley interactions. This is normal, as the Amber force field we are employing here does not use Urey-Bradley terms. A second warning states that our CRD file lacks velocities and box information will not be read. This is not a problem either, as we do not have velocities at this moment and box parameters are provided in the input file.
-In the next step we will perform 5 ps of dynamics in the NVT ensemble, to equilibrate the temperature of our simulation using this ''nvt.inp''. We are using the ''[inp>EXT_RESTART]'' section to restart with the last coordinates of the energy minimization procedure. Once the simulation has finished, take a look at the temperature file ''NVT-1.PARTICLES.temp'' to check that the temperature is oscillating around the correct value (in this case, 298K). Note that we are using the CSVR thermostat with a low time constant of 10 fs to efficiently and quickly control the system temperature. For production simulations a higher time constant such as 100 fs should be chosen to avoid interfering with the dynamics of the system.
+In the next step we will perform 5 ps of dynamics in the NVT ensemble, to equilibrate the temperature of our simulation using this ''nvt.inp''. We are using the ''[[inp>EXT_RESTART]]'' section to restart with the last coordinates of the energy minimization procedure. Once the simulation has finished, take a look at the temperature file ''NVT-1.PARTICLES.temp'' to check that the temperature is oscillating around the correct value (in this case, 298K). Note that we are using the CSVR thermostat with a low time constant of 10 fs to efficiently and quickly control the system temperature. For production simulations a higher time constant such as 100 fs should be chosen to avoid interfering with the dynamics of the system.
 The next step is simulating our system in the constant pressure NPT ensemble to get the correct dimensions for our cell. ''npt.inp'' runs 50 ps of NPT, outputting the cell dimensions into a separate file every 100 timesteps. A C-C distance in of the chorismate molecules is constrained, in order to keep it near the reactive conformation to facilitate our later simulations in the QM/MM phase. Pressure control is achieved by adding a barostat with a reference pressure of 1 bar and a coupling time of 100fs, and changing ''[[inp>MOTION/MD#ENSEMBLE]]'' from NVT to NPT_I, indicating that the box will be scaled isotropically. We expect our cell to shrink at first, as the solvation procedure cannot fill up the cell completely due to overlap with the protein and the edges of the box. After a while the cell size should stabilize. Take a look at the cell dimensions in ''NPT.cell''; we will be using these equilibrated cell dimensions for the next tutorial.