Fixed the execution order in OpenMM so that the generated trajectory frames correspon...

[alexxy/gromacs.git] / src / kernel / openmm_wrapper.cpp

diff --git a/src/kernel/openmm_wrapper.cpp b/src/kernel/openmm_wrapper.cpp
index 2fd6de3f58862942abf306f38eb7f49d5573e980..5a2aa22e0839d3bbaad290c9791c2808a35dcb1f 100644 (file)
--- a/src/kernel/openmm_wrapper.cpp
+++ b/src/kernel/openmm_wrapper.cpp
@@ -857,7 +857,7 @@ void* openmm_init(FILE *fplog, const char *platformOptStr,
         if (ir->nstcomm > 0)
             sys->addForce(new CMMotionRemover(ir->nstcomm));
 
-        // Set bonded force field terms.
+        /* Set bonded force field terms. */
         const int* bondAtoms = (int*) idef.il[F_BONDS].iatoms;
         HarmonicBondForce* bondForce = new HarmonicBondForce();
         sys->addForce(bondForce);
@@ -870,7 +870,8 @@ void* openmm_init(FILE *fplog, const char *platformOptStr,
             bondForce->addBond(atom1, atom2,
                                idef.iparams[type].harmonic.rA, idef.iparams[type].harmonic.krA);
         }
-        // Urey-Bradley includes both the angle and bond potential for 1-3 interactions
+
+        /* Urey-Bradley includes both the angle and bond potential for 1-3 interactions */
         const int* ubAtoms = (int*) idef.il[F_UREY_BRADLEY].iatoms;
         HarmonicBondForce* ubBondForce = new HarmonicBondForce();
         HarmonicAngleForce* ubAngleForce = new HarmonicAngleForce();
@@ -888,6 +889,8 @@ void* openmm_init(FILE *fplog, const char *platformOptStr,
             ubAngleForce->addAngle(atom1, atom2, atom3, 
                     idef.iparams[type].u_b.theta*M_PI/180.0, idef.iparams[type].u_b.ktheta);
         }
+
+               /* Set the angle force field terms */
         const int* angleAtoms = (int*) idef.il[F_ANGLES].iatoms;
         HarmonicAngleForce* angleForce = new HarmonicAngleForce();
         sys->addForce(angleForce);
@@ -901,6 +904,8 @@ void* openmm_init(FILE *fplog, const char *platformOptStr,
             angleForce->addAngle(atom1, atom2, atom3, 
                     idef.iparams[type].harmonic.rA*M_PI/180.0, idef.iparams[type].harmonic.krA);
         }
+
+               /* Set proper dihedral terms */
         const int* periodicAtoms = (int*) idef.il[F_PDIHS].iatoms;
         PeriodicTorsionForce* periodicForce = new PeriodicTorsionForce();
         sys->addForce(periodicForce);
@@ -917,6 +922,8 @@ void* openmm_init(FILE *fplog, const char *platformOptStr,
                                       idef.iparams[type].pdihs.phiA*M_PI/180.0, 
                                       idef.iparams[type].pdihs.cpA);
         }
+
+               /* Set improper dihedral terms that are represented by a periodic function (as in AMBER FF) */
         const int* periodicImproperAtoms = (int*) idef.il[F_PIDIHS].iatoms;
         PeriodicTorsionForce* periodicImproperForce = new PeriodicTorsionForce();
         sys->addForce(periodicImproperForce);
@@ -933,6 +940,8 @@ void* openmm_init(FILE *fplog, const char *platformOptStr,
                                       idef.iparams[type].pdihs.phiA*M_PI/180.0,
                                       idef.iparams[type].pdihs.cpA);
         }
+
+        /* Ryckaert-Bellemans dihedrals */
         const int* rbAtoms = (int*) idef.il[F_RBDIHS].iatoms;
         RBTorsionForce* rbForce = new RBTorsionForce();
         sys->addForce(rbForce);
@@ -950,6 +959,7 @@ void* openmm_init(FILE *fplog, const char *platformOptStr,
                                 idef.iparams[type].rbdihs.rbcA[4], idef.iparams[type].rbdihs.rbcA[5]);
         }
 
+               /* Set improper dihedral terms (as in CHARMM FF) */
         const int* improperDihAtoms = (int*) idef.il[F_IDIHS].iatoms;
                CustomTorsionForce* improperDihForce = new CustomTorsionForce("2.0*k*asin(sin((theta-theta0)/2))^2");
         sys->addForce(improperDihForce);
@@ -970,7 +980,7 @@ void* openmm_init(FILE *fplog, const char *platformOptStr,
                                 improperDihParameters);
         }
 
-        // Set nonbonded parameters and masses.
+        /* Set nonbonded parameters and masses. */
         int ntypes = fr->ntype;
         int* types = mdatoms->typeA;
         real* nbfp = fr->nbfp;