exercises:2014_ethz_mmm:alanine_dipeptide
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exercise:alanine_dipeptide [2014/04/21 15:33] – ibethune | exercise:alanine_dipeptide [2014/06/09 23:05] – dpasserone | ||
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In this exercise you will obtain a simplified version of the above potential energy surface, obtained in a very similar way as in the paper. You will constrain the angles at fixed values using a strong harmonic potential, and optimize all other degrees of freedom. From this, a grid of energies will be built, and the energy diagram (Ramachandran plot) will be constructed. | In this exercise you will obtain a simplified version of the above potential energy surface, obtained in a very similar way as in the paper. You will constrain the angles at fixed values using a strong harmonic potential, and optimize all other degrees of freedom. From this, a grid of energies will be built, and the energy diagram (Ramachandran plot) will be constructed. | ||
- | <note tip> Create a new directory for this exercise, and copy the files that you find in brutus in the directory / | + | <note tip> Create a new directory for this exercise, and copy there the files (** all commented **) that you can download |
< | < | ||
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The input file has a section concerning restrained optimization: | The input file has a section concerning restrained optimization: | ||
<code - inp.templ> | <code - inp.templ> | ||
- | & | + | & |
- | METHOD FIST | + | METHOD FIST ! Using Molecular Mechanics |
&MM | &MM | ||
- | & | + | & |
parm_file_name ace_ala_nme.pot | parm_file_name ace_ala_nme.pot | ||
- | | + | ! This file contains force field parameters |
- | & | + | |
- | EMAX_SPLINE 1.0 | + | & |
+ | ! in the nonboned interactions (both pair body potential and many body potential) | ||
+ | EMAX_SPLINE 1.0 ! Specify the maximum value of the potential up to which splines will be constructed | ||
&END | &END | ||
&END FORCEFIELD | &END FORCEFIELD | ||
- | & | + | & |
- | & | + | & |
- | EWALD_TYPE ewald | + | EWALD_TYPE ewald ! Standard non-fft based ewald method |
ALPHA .36 | ALPHA .36 | ||
- | GMAX 29 | + | GMAX 29 ! Number of grid points |
&END EWALD | &END EWALD | ||
&END POISSON | &END POISSON | ||
- | + | & | |
& | & | ||
&END | &END | ||
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&END | &END | ||
&END MM | &END MM | ||
- | & | + | & |
- | &CELL | + | & |
- | ABC 50.0 50.0 50.0 | + | ABC 50.0 50.0 50.0 ! Lengths of the cell vectors A, B, and C |
&END CELL | &END CELL | ||
- | & | + | & |
- | & | + | & |
- | ATOMS 5 7 9 15 ! | + | ATOMS 5 7 9 15 |
- | & | + | & |
& | & | ||
& | & | ||
&END | &END | ||
- | & | + | & |
- | & | + | & |
- | ATOMS 7 9 15 17 | + | ATOMS 7 9 15 17 ! Four atoms specify torsion angle |
& | & | ||
& | & | ||
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& | & | ||
CONN_FILE_NAME ace_ala_nme.psf | CONN_FILE_NAME ace_ala_nme.psf | ||
- | | + | ! File which contains the connectivity information |
+ | | ||
COORD_FILE_NAME ini.pdb | COORD_FILE_NAME ini.pdb | ||
- | | + | ! File which contains atom's coordinates of the system |
- | & | + | |
+ | & | ||
&END | &END | ||
- | & | + | & |
&END | &END | ||
&END TOPOLOGY | &END TOPOLOGY | ||
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&END SUBSYS | &END SUBSYS | ||
&END FORCE_EVAL | &END FORCE_EVAL | ||
- | + | & | |
- | & | + | PRINT_LEVEL LOW ! Global print level |
- | PRINT_LEVEL LOW | + | PROJECT ch ! Name of the project. This word will appear as part of a name of all ouput files (except main ouput file, specified with -o option) |
- | PROJECT ch | + | RUN_TYPE GEO_OPT |
- | RUN_TYPE GEO_OPT | + | |
&END GLOBAL | &END GLOBAL | ||
- | & | + | & |
- | & | + | & |
& | & | ||
INTERMOLECULAR T | INTERMOLECULAR T | ||
- | COLVAR 1 | + | COLVAR 1 ! Sequential number of the variable |
- | & | + | & |
- | K=5.0 | + | K=5.0 ! U(x)=K*(x-x0)^2 |
&END | &END | ||
- | TARGET [deg] _A1_ | + | TARGET [deg] _A1_ ! _A1_ will be changed to the number by an external scritp |
&END | &END | ||
& | & | ||
INTERMOLECULAR T | INTERMOLECULAR T | ||
- | COLVAR 2 | + | COLVAR 2 ! Sequential number of the variable |
- | & | + | & |
- | K=5.0 | + | K=5.0 ! U(x)=K*(x-x0)^2 |
- | &END | + | & |
- | TARGET [deg] _A2_ | + | TARGET [deg] _A2_ ! _A1_ will be changed to the number by an external scritp |
&END | &END | ||
& | & | ||
- | & | + | & |
& | & | ||
- | FORMAT PDB | + | FORMAT |
- | ADD_LAST NUMERIC | + | ADD_LAST NUMERIC |
&EACH | &EACH | ||
- | | + | |
&END | &END | ||
& | & | ||
& | & | ||
- | & | + | & |
- | OPTIMIZER BFGS | + | OPTIMIZER BFGS ! Type of the optimizer |
- | MAX_ITER 5000 | + | MAX_ITER 5000 ! Maximum number of optimization steps |
- | MAX_FORCE 0.005 | + | MAX_FORCE 0.005 ! The value of maximal force |
- | RMS_FORCE 0.003 | + | RMS_FORCE 0.003 ! The value of maximal force RMS |
& | & | ||
&END | &END | ||
+ | |||
</ | </ | ||
exercises/2014_ethz_mmm/alanine_dipeptide.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1