&cntrl namelist. See the sander module
input description for more information. Default is 0, which disables the
PME code.
PME requires extra input in order to
control the simulation. As in sander, this input,
consisting of three lines of free format numerical input
(not namelist input) palced just after the regular
namelist and before any weight change information.
LINE 1 Unit Cell parameters: BOXX,BOXY
BOXX,BOXY,BOXZ unit cell boxlengths in each dimension.
ALPHA,BETA,GAMMA unit cell angles, in usual crystallographic
setup. See sander documentation for more information.
LINE 2 Interpolation and control information: NFFT1,NFFT2,NFFT3,
SPLINE_ORDER,ISCHARGED,VERBOSE
NFFT1,NFFT2,NFFT3
These give the size of the grid to interpolate the
charge onto, in each dimension. See the discussion in
the Sander manual
SPLINE_ORDER
Order of the spline interpolation. See the sander manual.
ISCHARGED
If ISCHARGED=0, the unit cell is neutralized by taking the
excess charge and spreading it uniformly across all atoms.
If ISCHARGED=1, a uniform neutralizing plasma is assumed.
Note that in Gibbs, these operations are applied to the
unit cell at both the beginning and ending states of the
perturbation. Note that in some cases the charge state of
unit cell may change during the simulation, such as when
calculating the free energy of charging an ion. In these
cases it is better to use ISCHARGED=1.
VERBOSE
Standard use is to set VERBOSE=0. Setting VERBOSE=1 will
print out direct, self, adjustment and reciprocal
components of the energy and virial. Setting VERBOSE=3
will in addition print out details of the nonbond list.
LINE 3 The direct sum tolerance DSUM_TOL. See the discussion in Sander
manual.
- ---------------------------------------------------------
To summarize:
IELPER internals/vdw electrostatics
+1 fixed @ lambda=1 vary
(non-pert) values
-1 vary fixed @ lambda=0
(pert) values
---------------------------------------------------------
Mixing of electrostatic interactions done as
This is the default
Mixing of electrostatics done as
when Thermodynamic Integration is being performed (see
the IDIFRG flag, 14.6). This can be useful if the user wishes to apply an
alternative integration algorithm. Default is 0.
where r* is the optimal interaction distance between a pair of atoms, calculated from their respective van der Waals radii. This function is sometimes useful in structure refinement, but should *not* typically be used in free energy calculations. Atoms in the perturbed group are always treated by normal (6-12 or 10-12) non-bonded forces, regardless of the value of ISFTRP.
will be output at every energy update, so a different
integration algorithm can be applied by the user, if desired. If slow
growth has been requested, setting IDIFRG=1 has the effect of performing the
slow growth summation using the non-averaging equivalent of the TI equation
(4), rather than the FEP equation (2).
- i.e. #_windows < IAVSLM : dLAMBDA = ALMDL0
IAVSLM <= #_windows < IAVSLP :
dLAMBDA calculated from slope over #_windows
#_windows >= IAVSLP :
dLAMBDA calculated from slope over previous IAVSLP
windows
- AMXMOV, DLMIN, DLMAX, AMXRST, NTSD, ALMSTP(I)
FORMAT(4F14.9,I5,F14.9)
----------------------------------------------------------------
-- These card is read onlyif I3BOD.NE.0 --The GROUP input does not support a namelist convention.
This information must be provided in the formatted form given,
even if namelist format input is used above.
- 18A- 1) N3B, NION
FORMAT(2I5)
The number of 3body interactions to be defined, and the number
of ions in the system.
== Include N3N cards 18B to define all 3-body interactions ==.
- 18B- 1)AT1(I) 2)AT2(I) 3)ACON1(I) 4)BETA31(I) 5)GAMMA31(I)
6)ACON0(I) 7)BETA30(I) 8)GAMMA30(I)
FORMAT(A4,A4,2X,6E10.3)
AT1(I): The second atom in this 3-body interaction.
AT2(I): The third atom in this 3-body interaction.
ACON1(I): The pre-exponential factor for this 3-body
interaction for the lambda = 1 state.
BETA31(I): The beta value for this 3-body interaction,
for the lambda = 1 state.
GAMMA31(I): The gamma value for this 3-body interaction,
for the lambda = 1 state.
ACON0(I): The pre-exponential factor for this 3-body
interaction for the lambda = 0 state.
BETA30(I): The beta value for this 3-body interaction,
for the lambda = 0 state.
GAMMA30(I): The gamma value for this 3-body interaction,
for the lambda = 0 state.
----------------------------------------------------------------
- 19 - IDENTIFICATION OF ATOMS WITH POSITION CONSTRAINTS
*** ONLY IF NTR = 1 ***
Constraint reference atoms are obtained by first reading
coordinates for the entire structure through file 'PINCRD'
or 'PREFC', then specific constraint atoms are selected by
group. See the section on GROUP in the Appendices for format.
Does not support a namelist convention.
----------------------------------------------------------------
- 20 - IDENTIFICATION OF ATOMS FOR BELLY RUN
***** ONLY IF IBELLY .GT. 0 *****
The belly atoms are loaded as groups. Consult the GROUP section
in the Appendices for a description of how to define a group.
The group definition immediately follows the end of the &cntrl
namelist.
----------------------------------------------------------------
- 21 - DEFINITION OF GROUP INPUT FOR FREE ENERGY COMPONENTS
OR DERIVATIVES
***** (ONLY IF IPERAT = 4) *****
For free energy components, free energies will be logged
as defined by the GROUP definition, subject to the condition
that only those atoms which are part of the perturbed group
or which move with an added CONstraint will ultimately
be included. All atoms not explicitly included in a group
will be put in a final single group.
For free energy derivatives, derivatives will be logged
only for those atoms included in a group definition. Any
atom of the system may be designated as part of any group
(but each atom will be a member of at most one group).
Typically, you will place individual atoms in their own groups
when calculating derivatives.
Note that in GIBBS, GROUP input supports two new features that
can be helpful in defining the input for free energy components
or derivatives. Both allow the creation of multiple single-atom
groups:
ATOM -IAT1 IAT2
(1st atom number negative) will place each atom from IAT1 to
IAT2 in its own group.
RES -IRES1 -IRES2
(both residue numbers negative) will place each atom of every
residue in the range IRES1->IRES2 in a separate group.
Group definition syntax is otherwise the same as described in
the manual.
----------------------------------------------------------------
- 22 - DEFINITIONS OF INTERNAL RESTRAINTS/CONSTRAINTS
*** ONLY IF INTR > 0 (line 13) ***
BRIEF DESCRIPTION:
Setting INTR > 0 allows the user to define here a series of
internal restraints and constraints whose force constants and
equilibrium values are a function of lambda.
formatted form shown below, not in a namelist.
Restraints/constraints are read in as pairs of lines:
line A: IAT1,IAT2,IAT3,IAT4,IUMB,IZE,ITOR,RLMDA1,RLMDA2
FORMAT (7(I5,1X),2F10.5)
line B: RKEQ1,REQ1,RKEQ2,REQ2,IPER,IPER2
FORMAT (4F10.5,2I5)
As many restraints/constraints may be defined as are desired.
A blank record signals the end of the input. This data must be
entered in the formatted form shown.
INPUT VARIABLES
----- ---------
IAT1-->IAT4:
The absolute atom numbers for the atoms defining the restraint.
If an atom number is <0, the absolute value of the atom number
is used (additional behavior for <0 values is defined when
IZE=1; see below).
IAT3 = IAT4 = 0 : Bond restraints/constraints
IAT4 = 0 : Angle restraints/constraints
IAT1->IAT4 non-zero: Torsion restraints/constraints
RLMDA1
RLMDA2:The restraint/constraint will be applied only over the range in
lambda (RLMDA1, RLMDA2).
RKEQ1
REQ1 :The force constant in kcal/mol and equilibrium value,
respectively, for the restraint/constraint at lambda = RLMDA1.
RKEQ2
REQ2 :The force constant in kcal/mol and equilibrium value,
respectively, for the restraint/constraint at lambda = RLMDA2.
If RLMDA1=RLMDA2, the force constant and eq. value are fixed
at RKEQ1 and REQ1 (RKEQ2 and REQ2 are ignored).
RKEQ1 and RKEQ2 are ignored for constraints (ITOR=2).
If REQ1=999. or REQ2=999., the corresponding equilibrium value
is set to the current value of the internal coordinate (as
determined from the input set of coordinates PINCRD).
If ABS(REQ1) > 1000, the corresponding equilibrium value is set
REQ1 < 0: REQ1 = current_value - [ABS(REQ1)-1000.]
REQ1 > 0: REQ1 = current_value + [ABS(REQ1)-1000.]
If ABS(REQ2) > 1000, REQ2 is analogously reset.
Intermediate
and
are determined by linear interpolation between the force
constants and equilibrium values at RLMDA1 and RLMDA2.
No restraint/constraint is applied outside the range
(RLMDA1,RLMDA2).
IZE:
= 0 The restraint/constraint defined here is used _in addition to_
other parameters corresponding to this atom sequence from parm
(if any).
= 1 The restraint parameters defined here _replace_ overlapping
parameters from parm (if any) for this atom sequence.
When IZE=1, any atom number IAT1->IAT4 which was specified as
< 0 has a special meaning: It allows a "wildcard" match to the
corresponding atom number when replacing parameters from parm.
For example, the sequence -1 3 8 -14 would result in a torsional
restraint which would replace parameters for all torsions
centered on the bond between atoms 3 and 8.
IZE is read but ignored when ITOR=2 (constraints).
IUMB: Determines the type of restraint.
= 0 The restraint is to be considered part of the molecular force
field. The free energy contribution from the restraint is
calculated by the standard formula (c.f. Equation 2).
= 1 The restraint is considered to be an "umbrella" term. The
effects on the ensemble of the restraint are evaluated using
the following function in place of Equation 2:
where
is the sum of all umbrella restraint terms and
is as described for Equation 2.
IUMB is ignored for constraints (ITOR=2).
IUMB = 1 will not work correctly with slow growth or
thermodynamic integration.
ITOR: Functional form/constraint flag
= 0 If this is a torsional restraint, a potential of the form
is used. This functional form is always used for bonds and
angles (ITOR = 0 has no effect for bonds/angles).
= 1 If this is a torsional restraint, a potential of the form
is used. (ITOR = 1 has no effect for bonds/angles).
= 2 Then a constraint, rather than restraint, is applied to the
corresponding internal coordinate. This is applicable to all
types of internal coordinates (distances, angles, torsions).
If NCORC = 1 (line 9), then an effective "potential of mean
force" (PMF) contribution to the free energy will be calculated
for this internal coordinate.
General "holonomic" internal constraints are used, as described
in Reference 7.
When ITOR = 2 (internal is being constrained), IZE is ignored,
and the following occurs:
For bonds and angles, if the constrained internal matches an
internal in the topology file, force constant parameters
for matching internal will be set to 0.
For torsions, if the constrained internal matches an internal
in the topology file, A) forces for all torsions centered on
the same bond will be omitted B) The contributions to the
free energy of all torsions centered on the same bond as the
constraint will be calculated. This is necessary because
several torsions can be centered on a central bond, and
there is no fixed relative arrangement for these torsions.
IPER: IPER can be used to define a simulation where two internal
coordinates will be varied with two independent values of lambda.
Such a simulation can be used to generate a free energy
internal-internal map (sort of a free energy equivalent to a
Ramachandran map) to be generated.