The AGBNP3 implicit solvent model
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README.md

AGBNP3: Analytic Generalized-Born + Non-Polar model version 3

Emilio Gallicchio egallicchio@brooklyn.cuny.edu

Last Modified: May 2015

AGBNP is an analytical implicit solvent model based on the pairwise descreening (PD) Generalized Born (GB) model, a non-polar solvation free energy (NP) estimator, which takes into account independently the work of cavity formation and the solute-solvent van der Waals interaction energy, and a short-range solute-solvent hydrogen binding model. The model and its derivation are described in detail in the following paper:

Gallicchio E, Paris K, and Levy RM. The AGBNP2 Implicit Solvent Model. J Chem Theory Comput, 5, 2544-2564 (2009).

License

This software is released under the LGPL license. See LICENSE.

Credits

This software is written and maintained by Emilio Gallicchio egallicchio@brooklyn.cuny.edu with support from a grant from the National Science Foundation (ACI 1440665).

The AGBNP model has been developed by the author, Ronald M Levy ronlevy@temple.edu, and collaborators as described in the following publications:

Gallicchio E, Paris K, and Levy RM. The AGBNP2 Implicit Solvent Model. J Chem Theory Comput, 5, 2544-2564 (2009).

Gallicchio E., and R.M. Levy. AGBNP, an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling, J. Comp. Chem. 25, 479-499 (2004).

Portions of this software, limited to the driver file libagbnp3.c and the libnblist.c utility library, have been adapted from the AGBNP2 library written by the author while at Rutgers University in the group of Ronald M. Levy.

The sse_mathfun library has been written by Julien Pommier and released under the zlib license. See license declaration in sse_mathfun.h.

Installation

On a Linux system with gcc type make install in source directory. Link your code to the libagbnp3.a and libnblist.a libraries generated. Add the source directory to include path.

For example if the source directory is /src/AGBNP3 so

gcc -I/src/AGBNP3 mycode.c -o mycode -L/src/AGBNP3/ -lagbnp3 -lnblist

For other architecture and/or compilers modify the mach.macros file as needed.

AGBNP C API

The header file agbnp3.h must be included to access the AGBNP3 API functions.

 #include "agbnp3.h"
 > int agbnp_initialize( void );

Initializes libagbnp3 library. No library functions can be used until this call is made.

Return values: AGBNP_OK - library initialized OK. AGBNP_ERR - error in initialization.

 > void agbnp_terminate( void );

Terminates libagbnp3 library. Frees all associated storage. Once this call is made then the library can no longer be used until it is initialized again by calling agbnp_initialize().

typedef double float_i; //can be set to float, see agbnp3.h 
> int agbnp3_new(int *tag, int natoms, 
	      float_i *x, float_i *y, float_i *z, float_i *r, 
	      float_i *charge, float_i dielectric_in, float_i dielectric_out,
	      float_i *igamma, float_i *sgamma,
	      float_i *ialpha, float_i *salpha,
	      int *hbtype, float_i *hbcorr,
	      int nhydrogen, int *ihydrogen, 
	      NeighList *conntbl,
	      int verbose);

Creates a new instance of AGBNP3. If successful this function returns in the 'tag' argument a non-negative integer id that identifies the instance. All subsequent operations on this instance should reference this tag. Any number of AGBNP3 instances can be generated by calling the agbnp3_new() function. Each instance is independent from the others, that is each may correspond to different systems, parameters, etc.

Input parameters (units in []):

natoms: number of atoms of the system. Atoms are numbered from 0 to natoms-1.

x, y, z: Cartesian coordinates of each atom [Angstroms].

r: van der Waals radius of each atom [Angstroms]

charge: partial charge of each atom [e].

dielectric_in: value of the interior (solute) relative dielectric constant.

dielectric_out: value of the exterior (solvent) relative dielectric constant.

igamma: value of the gamma non-polar parameter for each atom [(kcal/mol)/Ang^2]

sgamma: value of the gamma non-polar correction parameter for each atom [(kcal/mol)/Ang^2]

ialpha: value of the "alpha" van der Waals non-polar parameter for each atom [(kcal/mol) Ang^3]

salpha value of the "alpha" van der Waals non-polar correction parameter for each atom [(kcal/mol) Ang^3]

Note: The values of the non-polar parameters used internally are the sum of the ideal and correction values. However the non-polar energy derived from each is reported separately as a pure non-polar energy and a correction energy term. If you are confused about this just set the correction parameters to zero.

hbtype: hydrogen bonding type for each type, one of the AGBNP_HB_* atom geometry identifiers listed in agbnp3.h

hbcorr: hydrogen bonding strength parameter [kcal/mol]

nhydrogen: number of hydrogen atoms in the system.

ihydrogen: atom index of each hydrogen atom. Note that atom indexes start from zero.

conntbl: atom connection table. It lists the atoms directly bonded to each atom. It is specified in terms a neigh_list structure defined with the libnblist library - included in the AGBNP3 distribution. For documentation pertaining to libnblist see below.

Return values: AGBNP_OK - AGBNP instance created, id tag is returned in 'tag'. AGBNP_ERR - error creating AGBNP instance. Consult error message on stderr.

> int agbnp_delete(int tag);

Deletes the AGBNP instance referenced by 'tag'. Associated memory is freed.

Return values: AGBNP_OK - AGBNP instance deleted. AGBNP_ERR - error deleting AGBNP instance. Consult error message on stderr.generalized born and van der Waals energies

int agbnp3_ener(int tag, int init,
		float_i *x, float_i *y, float_i *z,
		float_i *sp, float_i *br, 
		float_i *mol_volume, float_i *surf_area, 
		float_i *egb, float_i (*dgbdr)[3],
		float_i *evdw, float_i *ecorr_vdw, float_i (*dvwdr)[3], 
		float_i *ecav, float_i *ecorr_cav, float_i (*decav)[3],
		float_i *ehb,  float_i (*dehb)[3]);

Calculates energies and derivatives of instance referenced by tag.

Input parameters:

init: unused

x, y, z: current atomic positions [Angstroms]

sp: atomic volume scaling factor

br: Born radius [Angstroms]

mol_volume: molecular volume

surf_area: solvent-exposed surface area of each atom [Ang^2]

egb: generalized Born energy [kcal/mol]

evdw, ecorr_vdw: solute solvent van der Waals energy [kcal/mol]

ecav, ecorr_cav: cavity energy [kcal/mol]

ehb: solute-solvent hydrogen bonding energy [kcal/mol]

dgbdr, dvwdr, decav, dehb: gradients of egb, evdw, ecav and ehb.

Return values: AGBNP_OK - AGBNP energy calculated. AGBNP_ERR - Error calculating energy. Consult error message on stderr.

Verlet Neighbor List Utility Functions (libnblist)

The libnblist library provides a data structure to hold a Verlet neighbor list and a set of utility functions to manage the memory associated with the Verlet neighbor list.

To use this facility the libnblist header file must be included

 #include "libnblist.h"

this file is automatically included by agbnp.h

libnblist defines the NeighList data type, a C structure composed of the following members:

  • Core members:

    int natoms; number of atoms.

    int neighl_size; Holds the allocated size of the Verlet neighbor list, this is the maximum number of neighbors that can be stored in the list.

    int *nne; an array of size natoms that holds the number of neighbors for each atom.

    int *neighl1; the pointer to the memory space where the neighbor list is actually stored.

    int **neighl; an array of pointers into neighl1 of size natoms pointing to the start of the list of neighbors for each atom. So for example, neighl[iat][j], 0 <= j < nne[iat], are the atom indexes of the neighbors of atom iat.

  • Atom indexes remapping members:

    int idx_remap; whether (yes > 0, no = 0) to do atom indexes remapping.

    int *int2ext; an optional array of size natoms to translate from internal to external atom indexes.

    int *ext2int; an optional array of size max(external index)+1 to translate from external to internal atom indexes.

    Note: libnblist can be used to store Verlet neighbor lists for calling programs using different atom indexing schemes - starting from zero, starting from one, random, etc . To do so libnblist makes a distinction between internal and external atom indexes. This is best illustrated with an example. Let us say that in the caller program 5 atoms are defined with atomic indexes 7, 9, 4, 6, and 2. The neighbor lists for these atoms are stored in the Verlet neighbor list in this order so that neighl[0][j] identifies the neighbors of atom 7, neighl[1][j] identifies the neighbors of atom 9, etc. 0 is the internal index for atom 7, 1 is the internal atom index for atom 9, etc. In order to reference and dereference the neighbor list mapping arrays are constructed. The content of the int2ext array in this case would be:

    int2ext = { 7, 9, 4, 6, 2 };

    and the content of the ext2int array would be:

    ext2int = { -, -, 4, -, 2, -, 3, 0, -, 1 };

    So that for example int2ext[4] = 2 and ext2int[9] = 1. The neighbors of atom 9 are neighl[ext2int[9]][j], 0 <= j < nne[ext2int[9]]. The Verlet neighbor list stores the external atom indexes of the neighbors so that for example in iat = neighl[ext2int[9]][1], iat may be 6. AGBNP uses the libnblist indexes remapping arrays to convert from internal AGBNP atom indexes (which start from 0 and end at natoms-1) to external atom indexes (that could be anything) and viceversa. It is the responsibility of the caller to properly set up the remapping arrays.

  • Other data:

    The libnblist data structure has place holders for other types of data (Periodic Boundary Conditions translation vectors and general additional data). These data structures are not described here as they are not relevant to AGBNP usage.

Libnblist C API

libnblist provides simple memory management functions for Verlet neighbor lists.

The caller usually creates a libnblist structure by allocating memory for it:

 NeighList *nl;
 nl = (NeighList *)malloc(sizeof(NeighList));

nl is then used as an argument for the utility functions that follow.

 > void nblist_reset_neighbor_list(NeighList *neigh_list);

resets structure to pristine state. All pointers NULL, variables set to zero.

 > int nblist_reallocate_neighbor_list(NeighList *nl, int natoms, int nlsize);

Reallocates memory for the Verlet neighbor list pointed by 'nl'. 'natoms' is the new number of atoms and 'nlsize' is the new list size. If natoms > nl->natoms the list is resized in terms of the number of atoms. If nlsize > nl->neighl_size the size of the Verlet neighbor list is reallocated as well. In either case the previous contents of the neighbor list structure are preserved, including index remapping arrays and additional data. Return values: NBLIST_OK - Neighbor list memory reallocated. NBLIST_ERR - Error reallocating memory for neighbor list. Neighbor list may be unusable at this point. Consult error messages on stderr.

 > int nblist_delete_neighbor_list(NeighList *nl);

Frees memory associated with the Verlet neighbor list referenced by 'nl'. The memory associated with the neighbor list structure itself is not freed. The calling program is responsible for calling free(nl) if needed. Return values: NBLIST_OK - Neighbor list memory freed. NBLIST_ERR - Error freeing memory of neighbor list. Consult error messages on stderr.