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--- exercise:alanine_dipeptide [2014/04/21 15:33] – ibethune
+++ exercise:2014_ethz_mmm:alanine_dipeptide [2014/10/15 13:26] – oschuett
@@ Line 3: / Line 3: @@
 Alanine dipeptide is often studied in theoretical work because it is among the simplest systems to exhibit some of the important features common to biomolecules. It has more than one long-lived conformational state. The relevant angles are the dihedral angles of the backbone, commonly called Φ and Ψ (see figure). In the following scheme, light blue atoms are carbons, white ones are hydrogens, red are oxygens, and blue are nitrogens. So the torsional angle Φ is C-N-C-C and Ψ is N-C-C-N along the backbone.
-{{ :exercise:alanine.png?direct&400 |}}
+{{ alanine.png?direct&400 |}}
 A detailed study of this system (see [[doi>10.1073/pnas.100127697]]) shows the presence, in vacuum of two stable states:
@@ Line 13: / Line 13: @@
 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 /cluster/home03/matl/danielep/LECTURE2/EXERCISE_2.2 or downloaded from the wiki: {{exercise:exercise_2.2.tar.gz|exercise_2.2.tar.gz}}</note>
+<note tip> Create a new directory for this exercise, and copy there the files (** all commented **) that you can download from the wiki: {{exercise:exercise_2.2.zip|exercise_2.2.zip}}</note>
 <code>
@@ Line 23: / Line 23: @@
 The input file has a section concerning restrained optimization:
 <code - inp.templ>
-&FORCE_EVAL
+&FORCE_EVAL                             ! This section defines method for calculating energy and forces
-  METHOD FIST
+  METHOD FIST                           ! Using Molecular Mechanics
   &MM
-    &FORCEFIELD
+    &FORCEFIELD                         ! This section specifies forcefield parameters
       parm_file_name ace_ala_nme.pot
-      parmtype CHM
+! This file contains force field parameters
-      &SPLINE
+      parmtype CHM                      ! forcefield parameters has CHARMM format
-        EMAX_SPLINE 1.0
+      &SPLINE           ! This section specifies parameters to set up the splines used
+! 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 FORCEFIELD
-    &POISSON
+    &POISSON                            ! This section specifies parameters for the Poisson solver
-      &EWALD
+      &EWALD                            ! This section specifies parameters for the EWALD summation method (for the electrostatics)
-        EWALD_TYPE ewald
+        EWALD_TYPE ewald                ! Standard non-fft based ewald method
         ALPHA .36
-        GMAX 29
+        GMAX 29                         ! Number of grid points
       &END EWALD
     &END POISSON
-    &PRINT
+    &PRINT                              ! This section controls printing options
       &FF_INFO
       &END
@@ Line 47: / Line 49: @@
     &END
   &END MM
-  &SUBSYS
+  &SUBSYS                               ! This section defines the system
-    &CELL
+    &CELL                               !  Unit cell set up
-      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
-    &COLVAR                        ! DEFINITION OF THE DIHEDRALS
+    &COLVAR                             ! This section specifies collective varialbe
-       &TORSION                    !
+       &TORSION                         ! This section defines variable as torsion angle
-         ATOMS 5 7 9 15            !
+         ATOMS 5 7 9 15                 ! Four atoms specify torsion angle
-       &END                        !
+       &END
        &PRINT
        &END
     &END
-    &COLVAR
+    &COLVAR                             ! This section specifies collective varialbe
-       &TORSION
+       &TORSION                         ! This section defines variable as torsion angle
-         ATOMS 7 9 15 17
+         ATOMS 7 9 15 17                ! Four atoms specify torsion angle
        &END
        &PRINT
@@ Line 67: / Line 69: @@
      &TOPOLOGY
       CONN_FILE_NAME ace_ala_nme.psf
-      CONNECTIVITY psf
+! File which contains the connectivity information
+      CONNECTIVITY psf                  ! Format of the connectivity file is PSF
       COORD_FILE_NAME ini.pdb
-      COORDINATE PDB
+! File which contains atom's coordinates of the system
-      &DUMP_PDB
+      COORDINATE PDB                    ! Coordinates are in the PDB format
+      &DUMP_PDB                         ! This sections specifies the dumping of the PDB at the starting geometry
       &END
-      &DUMP_PSF
+      &DUMP_PSF                         ! This sections specifies the dumping of the PSF connectivity
       &END
     &END TOPOLOGY
@@ Line 82: / Line 86: @@
   &END SUBSYS
 &END FORCE_EVAL
+&GLOBAL                                 ! Section with general information regarding which kind of simu lation to perform an parameters for the whole PROGRAM
-&GLOBAL
+  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 is a geometry optimization
-  RUN_TYPE GEO_OPT
 &END GLOBAL
-&MOTION
+&MOTION                                 ! This section specifies a set of tool connected with the motion of the nuclei
- &CONSTRAINT
+ &CONSTRAINT                            ! Section specifying information regarding how to impose constraints on the system
   &COLLECTIVE
   INTERMOLECULAR T
-    COLVAR 1
+    COLVAR 1                            ! Sequential number of the variable
-    &RESTRAINT                   ! RESTRAINT ON THE COLLECTIVE VARIABLE 1 WITH A LARGE SPRING CONSTANT
+    &RESTRAINT                          ! This section specifies how stong is the restraint
-      K=5.0
+      K=5.0                             ! U(x)=K*(x-x0)^2
     &END
-    TARGET [deg] _A1_
+    TARGET [deg] _A1_                   ! _A1_ will be changed to the number by an external scritp
   &END
    &COLLECTIVE
   INTERMOLECULAR T
-    COLVAR 2
+    COLVAR 2                            ! Sequential number of the variable
-    &RESTRAINT
+    &RESTRAINT                          ! This section specifies how stong is the restraint
-      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
- &PRINT
+ &PRINT                                 ! This section controls the printing properties during an optimization or MD run
    &TRAJECTORY
-    FORMAT PDB
+    FORMAT PDB                          ! Format of  the ouput trajectory is PDB
-    ADD_LAST NUMERIC
+    ADD_LAST NUMERIC                    ! (Wiki) If the last iteration should be added, and if it should be marked symbolically (with l) or with the iteration number.Not every iteration level is able to identify the last iteration early enough to be able to output. When this keyword is activated all iteration levels are checked for the last iteration step.
     &EACH
-     GEO_OPT 100
+     GEO_OPT 100                        ! Print one frame every 100 iteration
     &END
    &END
  &END
- &GEO_OPT
+ &GEO_OPT                               ! This section specifies optimizer options
-    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
 </code>