overlap (c49b1)
Overlap of Molecular Similarity
This is a maximum overlap method to investigate the structural
similarity of flexible molecules. The atoms are described as Gaussians
and the interaction energy between different molecules are basically
overlap integrals. The Gaussians can represent either volume or charge.
Alternatively, the overlap of the electrostatic potential is provided
yielding exponential form.
This method supports all CHARMM functionality, because it provides
just another energy term and forces for it. Only periodic boundaries and
VIBRAN are not supported.
Refercence: :Juneja, A; Riedesel, H; Hodoscek, M ; Knapp, EW
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009) 5, 659-673
* Description | Description of the OVERLAP commands.
* Usage | How to use the OVERLAP method.
* Implementation | Implementation of the OVERLAP method
* Performance | Performance Issues
This is a maximum overlap method to investigate the structural
similarity of flexible molecules. The atoms are described as Gaussians
and the interaction energy between different molecules are basically
overlap integrals. The Gaussians can represent either volume or charge.
Alternatively, the overlap of the electrostatic potential is provided
yielding exponential form.
This method supports all CHARMM functionality, because it provides
just another energy term and forces for it. Only periodic boundaries and
VIBRAN are not supported.
Refercence: :Juneja, A; Riedesel, H; Hodoscek, M ; Knapp, EW
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009) 5, 659-673
* Description | Description of the OVERLAP commands.
* Usage | How to use the OVERLAP method.
* Implementation | Implementation of the OVERLAP method
* Performance | Performance Issues
Top
SYNTAX and DESCRIPTION
======================
One command (OLAP) is used in several different forms to specify
everything.
To initialize the method use:
OverLAP NUMB <int> WEIGht <real> VOLW <real> CHAW <real> ESPW <real> -
WIDTh <real> GAMMa <real> WEPO <real>
NUMB <int> - how many subsystems do we have
WEIG <real> - weighting factor for the whole overlap term; it also
accounts to bring units to kcal/mol, default = 1.0
VOLW <real> - weighting factor for the volume overlap term,
default = 0.0
CHAW <real> - weighting factor for the partial atomic charge overlap
term, default = 0.0
ESPW <real> - weighting factor for the electrostatic potential
overlap term, default = 0.0
NOTE: Since all these three individual weighting factors default to 0.0,
the user has to specify at least one of them as a non-zero value, or the
program will bomb out because there is no overlap to calculate!
The overall overlap Hodgkin index is calculated according to the following
formula:
VOLW * H(volume) + CHAW * H(charge) + ESPW * H(e-s.pot)
H(total) = -------------------------------------------------------
VOLW + CHAW + ESPW
This way the overall Hodgkin index will be scaled between -1 and 1, no
matter what are the values of the individual weighting factors.
WIDT <real> - this value is used to scale all the atomic radii when
calculating volume or electrostatic potential overlap,
default = 1.0
GAMM <real> - gamma value for the electrostatic potential, default = 1.0
WEPO <real> - linear factor for the electrostatic potential,
default = 1.0
Before this initial OLAP command is called, WMAIN array should contain
partial atomic charges. In the course of initializing the overlap
subsystem, these charges will be copied from WMAIN to an internal array.
After the initialization, the user should load WMAIN with per-atom
weighting factors for the volume overlap (if the volume overlap is to be
used at all). The most simple way to do this is via:
SCALAR WMAIN SET 1
which will give equal weighting of 1.0 to all atoms. Be aware of the
commands that could alter WMAIN array so that these weighting factors
are lost before calculating the overlap energy term!
After initialization, subsystems should be defined using the following
command:
OLAP SYST <int> WEIG <real> SELE <selection factor> END
SYST <int> - the number of the subsystem being defined, should be
in range from 1 to the number given in the initialization
command (NUMB parameter)
WEIG <real> - weighting factor for the system being defined,
default = 1.0
SELE ... END - selection of atoms which constitute this system.
The memory usage for these selections of subsystems is specified
dynamically so there can be as many as one needs of these lines.
Do not forget to cancel all physical energy terms between subsystems
treated with the OLAP! This can be done using BLOCK command. Here is an
example for three subsystems:
BLOCK 3
CALL 2 SELE ... END
CALL 3 SELE ... END
COEF 1 2 0.0
COEF 1 3 0.0
COEF 2 3 0.0
END
[For more than several subsystems, there will be many ``COEF x y 0.0''
lines. This is something which may change, since specifying many block
commands may cause users to make errors.
Possible solutions:
1. When generating nonbond list check the following:
if ((nolap(i).gt.0).and.(nolap(j).gt.0))then
if (iolap(nolap(i)).ne.iolap(nolap(j))) then
these 2 atoms have to be excluded.
endif
endif
2. Or put the above in the exclusion list ??
3. or use block code - this works!
To check which atom is in which subsystem one can use:
OLAP PRINt
To print out individual forces and separate volume, charge and
electrostatic potential Hodgkin indices use:
OLAP DEBUg - turn on debugging
OLAP NODEbug - turn off debugging
NOTE: This produces huge output! Therefore, it is not recomended to turn
debugging on before a minimization or a dynamics run.
Weighting factors for the overlap terms (WEIG, VOLW, CHAW, ESPW) and
factors determining the shape of Gaussian and exponential functions
(WIDT, GAMMa, WEPO) can be changed via:
OLAP RESTart WEIG <real> VOLW <real> CHAW <real> ESPW <real> -
WIDT <real> GAMMa <real> WEPO <real>
For the description of OLAP REST parameters, see above the section on
initializing.
NOTE: When utilizung OLAP REST command, default values of all parameters
are not the previous ones, but the general defaults (VOLW=0, CHAW=0,
ESPW=0, WIDT=1, GAMM=1, WEPO=1)! Therefore, the user has to specify all
the non-default values again.
To turn off the overlap method completely, use:
OverLAP OFF
NOTE: This command also copies charges back to WMAIN!
SYNTAX and DESCRIPTION
======================
One command (OLAP) is used in several different forms to specify
everything.
To initialize the method use:
OverLAP NUMB <int> WEIGht <real> VOLW <real> CHAW <real> ESPW <real> -
WIDTh <real> GAMMa <real> WEPO <real>
NUMB <int> - how many subsystems do we have
WEIG <real> - weighting factor for the whole overlap term; it also
accounts to bring units to kcal/mol, default = 1.0
VOLW <real> - weighting factor for the volume overlap term,
default = 0.0
CHAW <real> - weighting factor for the partial atomic charge overlap
term, default = 0.0
ESPW <real> - weighting factor for the electrostatic potential
overlap term, default = 0.0
NOTE: Since all these three individual weighting factors default to 0.0,
the user has to specify at least one of them as a non-zero value, or the
program will bomb out because there is no overlap to calculate!
The overall overlap Hodgkin index is calculated according to the following
formula:
VOLW * H(volume) + CHAW * H(charge) + ESPW * H(e-s.pot)
H(total) = -------------------------------------------------------
VOLW + CHAW + ESPW
This way the overall Hodgkin index will be scaled between -1 and 1, no
matter what are the values of the individual weighting factors.
WIDT <real> - this value is used to scale all the atomic radii when
calculating volume or electrostatic potential overlap,
default = 1.0
GAMM <real> - gamma value for the electrostatic potential, default = 1.0
WEPO <real> - linear factor for the electrostatic potential,
default = 1.0
Before this initial OLAP command is called, WMAIN array should contain
partial atomic charges. In the course of initializing the overlap
subsystem, these charges will be copied from WMAIN to an internal array.
After the initialization, the user should load WMAIN with per-atom
weighting factors for the volume overlap (if the volume overlap is to be
used at all). The most simple way to do this is via:
SCALAR WMAIN SET 1
which will give equal weighting of 1.0 to all atoms. Be aware of the
commands that could alter WMAIN array so that these weighting factors
are lost before calculating the overlap energy term!
After initialization, subsystems should be defined using the following
command:
OLAP SYST <int> WEIG <real> SELE <selection factor> END
SYST <int> - the number of the subsystem being defined, should be
in range from 1 to the number given in the initialization
command (NUMB parameter)
WEIG <real> - weighting factor for the system being defined,
default = 1.0
SELE ... END - selection of atoms which constitute this system.
The memory usage for these selections of subsystems is specified
dynamically so there can be as many as one needs of these lines.
Do not forget to cancel all physical energy terms between subsystems
treated with the OLAP! This can be done using BLOCK command. Here is an
example for three subsystems:
BLOCK 3
CALL 2 SELE ... END
CALL 3 SELE ... END
COEF 1 2 0.0
COEF 1 3 0.0
COEF 2 3 0.0
END
[For more than several subsystems, there will be many ``COEF x y 0.0''
lines. This is something which may change, since specifying many block
commands may cause users to make errors.
Possible solutions:
1. When generating nonbond list check the following:
if ((nolap(i).gt.0).and.(nolap(j).gt.0))then
if (iolap(nolap(i)).ne.iolap(nolap(j))) then
these 2 atoms have to be excluded.
endif
endif
2. Or put the above in the exclusion list ??
3. or use block code - this works!
To check which atom is in which subsystem one can use:
OLAP PRINt
To print out individual forces and separate volume, charge and
electrostatic potential Hodgkin indices use:
OLAP DEBUg - turn on debugging
OLAP NODEbug - turn off debugging
NOTE: This produces huge output! Therefore, it is not recomended to turn
debugging on before a minimization or a dynamics run.
Weighting factors for the overlap terms (WEIG, VOLW, CHAW, ESPW) and
factors determining the shape of Gaussian and exponential functions
(WIDT, GAMMa, WEPO) can be changed via:
OLAP RESTart WEIG <real> VOLW <real> CHAW <real> ESPW <real> -
WIDT <real> GAMMa <real> WEPO <real>
For the description of OLAP REST parameters, see above the section on
initializing.
NOTE: When utilizung OLAP REST command, default values of all parameters
are not the previous ones, but the general defaults (VOLW=0, CHAW=0,
ESPW=0, WIDT=1, GAMM=1, WEPO=1)! Therefore, the user has to specify all
the non-default values again.
To turn off the overlap method completely, use:
OverLAP OFF
NOTE: This command also copies charges back to WMAIN!
Top
USAGE
=====
Since everything is flexible, I suggest to start with aligning the
systems to themself first. With this approach one gets the estimate of
the weights and radii which can be later used and improved in the
alignement process of different species.
It is sometimes usefull to exclude certain atoms from the alignement
procedure. The obvious procedure to do this is to use SCALar command
and assign the WMAIN array to zero. This can be done both before
OLAP initialization (thus setting atomic charges to zero and excluding
them from the charge and electrostatic potential overlap) and after
it (thus excluding atoms from the volume overlap).
USAGE
=====
Since everything is flexible, I suggest to start with aligning the
systems to themself first. With this approach one gets the estimate of
the weights and radii which can be later used and improved in the
alignement process of different species.
It is sometimes usefull to exclude certain atoms from the alignement
procedure. The obvious procedure to do this is to use SCALar command
and assign the WMAIN array to zero. This can be done both before
OLAP initialization (thus setting atomic charges to zero and excluding
them from the charge and electrostatic potential overlap) and after
it (thus excluding atoms from the volume overlap).
Top
IMPLEMENTATION
==============
This is a new area of research, and the user might want to play with
the different ``energy'' terms or formulas. The following is a
guideline to do that. Everything CHARMM related is separated from the
energy routines, so it should be easy for anyone to adjust the
formulas for the systems under investigation.
Because in general we may have one atom in several systems we need to
use the following data structure:
NOLAP(i), i=1, NATOM this is a vector of pointers to the IOLAP array.
IOLAP(i), i=1, NOLAP(NATOM) this is a vector which contains the information
to which subsystem each atom belongs to.
Then the loop for the overlap integrals would be like this:
do i = 1, natom
do j = 1, natom
do k = nolap(i),nolap(i+1)-1
ix=iolap(k)
if(ix.gt.0) then
do l = nolap(j), nolap(j+1)-1
jx=iolap(l)
if(jx.gt.0) then
ipt = (ix-1)*ix/2+jx ! this is not general case
s(ipt) = s(ipt) + gauss(i)*gauss(j)
endif
enddo
endif
enddo
enddo
enddo
The above is simplified model for illustration purposes only. For
details see the actual code. All the code for calculating overlap
energies and forces is in energy/eolap.src; command-line analysis is
in misc/olap.src. Also see fcm/olap.fcm.
The keyword to compile the method is ##OVERLAP.
IMPLEMENTATION
==============
This is a new area of research, and the user might want to play with
the different ``energy'' terms or formulas. The following is a
guideline to do that. Everything CHARMM related is separated from the
energy routines, so it should be easy for anyone to adjust the
formulas for the systems under investigation.
Because in general we may have one atom in several systems we need to
use the following data structure:
NOLAP(i), i=1, NATOM this is a vector of pointers to the IOLAP array.
IOLAP(i), i=1, NOLAP(NATOM) this is a vector which contains the information
to which subsystem each atom belongs to.
Then the loop for the overlap integrals would be like this:
do i = 1, natom
do j = 1, natom
do k = nolap(i),nolap(i+1)-1
ix=iolap(k)
if(ix.gt.0) then
do l = nolap(j), nolap(j+1)-1
jx=iolap(l)
if(jx.gt.0) then
ipt = (ix-1)*ix/2+jx ! this is not general case
s(ipt) = s(ipt) + gauss(i)*gauss(j)
endif
enddo
endif
enddo
enddo
enddo
The above is simplified model for illustration purposes only. For
details see the actual code. All the code for calculating overlap
energies and forces is in energy/eolap.src; command-line analysis is
in misc/olap.src. Also see fcm/olap.fcm.
The keyword to compile the method is ##OVERLAP.
Top
PERFORMANCE ISSUES
==================
(since the systems are usually small this is not so big issue)
Very probably the method is trivial to parallelize. The following
should take care of it:
In OLAPINT()
icalc=0
do i = 1, natom
do j = 1, natom
....
icalc=icalc+1
if(mod(icalc,numnod).eq.mynod) then
...
call fmgauss()
...
endif
....
enddo
enddo
This is a scheme for perfect load balance. However there is some loss
in olapsd, because it always does it for all atoms (it doesn't scale)
This way there is no additional communication involved!!!?
PERFORMANCE ISSUES
==================
(since the systems are usually small this is not so big issue)
Very probably the method is trivial to parallelize. The following
should take care of it:
In OLAPINT()
icalc=0
do i = 1, natom
do j = 1, natom
....
icalc=icalc+1
if(mod(icalc,numnod).eq.mynod) then
...
call fmgauss()
...
endif
....
enddo
enddo
This is a scheme for perfect load balance. However there is some loss
in olapsd, because it always does it for all atoms (it doesn't scale)
This way there is no additional communication involved!!!?