![]() It takes ~30 seconds to complete the calculation. The actual number of availavle CPU cores depends on the user’s computer environment and should be set to an appropriate value by the user (see the Usage page for details). The following command uses 4 MPI processors and 4 OpenMP threads, i.e., a total of 16 CPU cores. Let’s run energy minimization using spdyn. Nbupdate_period = 10 # nonbond update periodīox_size_x = 50.2 # box size (x) in īox_size_y = 50.2 # box size (y) in īox_size_z = 50.2 # box size (z) in Rstout_period = 2000 # restart output period Nsteps = 2000 # number of minimization stepsĮneout_period = 50 # energy output periodĬrdout_period = 50 # coordinates output period Vdw_force_switch = YES # force switch option for van der WaalsĬontact_check = YES # check atomic clash method = SD # 1_setup/3_solvate/wbox.pdb # PDB fileĭcdfile = min.dcd # DCD trajectory file rstfile = min.rst # restart file 1_setup/3_solvate/wbox.psf # protein structure file toppar/toppar_water_ions.str # stream file toppar/par_all36m_prot.prm # parameter file strfile =. toppar/top_all36_prot.rtf # topology file This file will be used as the input file for the subsequent MD simulation. Here, the rstfile is a “restart file” and contains the coordinates of the atoms at the final step of the energy minimization. In the section, dcdfile and rstfile are specified. Therefore, another file ( toppar_water_ions.str) containing topology and parameters for water and ions is further passed to the section. However, information on water and ions is not included in these files. The top_all36_prot.rtf and par_all36m_prot.prm specified in the section contain only the force field parameters for amino acids. In the same section, you can find “ contact_check = YES“, which is usually essential to avoid instabilities in the early stages of the energy minimization (for details, see the User manual). This combination of switch and cutoff distances has recently been recommended for MD simulations using the CHARMM C36 force field and explicit solvent. A cutoff distance of 12.0 Å is used for non-bonded interactions and a switching distance of 10.0 Å is used for van der Waals interactions. The particle mesh Ewald method (PME) is employed to calculate long-range interactions and is specified by electrostatic = PME in the section. Since the system has a periodic boundary condition and the total charge is zero, the Ewald method can be used. Since the target system has a periodic boundary condition (PBC), we set type = PBC in the section and also set the initial box size with box_size = 50.2. Here, the steepest descent (SD) method is used to perform a 2,000-steps energy minimization. In the section of the control file, we specify the method to be used in the energy minimization. /2_minimize # View the control file $ less INP # Change directory for the energy minimization $ cd. Let’s change the directory to perform energy minimization and look at the GENESIS control file. One of the most popular methods is the steepest descent method, which is introduced in GENESIS. In general, energy minimization is a method of minimizing the potential energy of the system by simply moving the atoms gradually in the direction of the force acting on them. However, in most cases, energy minimization must be performed before MD simulations to remove atomic clash in the initial structure. In the previous tutorial ( Tutorial 3.1), we just performed MD simulation. $ build.tcl log wbox.log wbox.pdb wbox.psf # View the initial structure # Change directory for the system setupīuild.tcl log proa.pdb proa.psf # Solvate the peptide in water ![]() The total number of atoms in this system is about 12,000. ![]() We obtain wbox.pdb and wbox.psf as input files for GENESIS. The peptide is solvated in a water box (50.2 Å × 50.2 Å × 50.2 Å). This scheme is identical to Steps 1, 3, and 4 in Tutorial 2.3. First, we build a system using VMD/PSFGEN from a PDB file of the (Ala) 3 and the CHARMM topology file. In this tutorial, we will simulate (Ala) 3 in water. binġ_setup 2_minimize 3_equilibrate 4_production 5_analysis bin toppar $ echo "tutorial-3.2: MD simulation of Ala3 in water" > README # Put the tutorial file in the Works directory Since we use the CHARMM36m force field parameters, we make a symbolic link to the CHARMM toppar directory (see Tutorial 2.2). Control files for GENESIS are already included in the download file. This tutorial consists of five steps: 1) system setup, 2) energy minimization, 3) equilibration, 4) production run, and 5) trajectory analysis. Let’s download the tutorial file ( tutorial22-3.2.zip). ![]()
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