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From: FyD <fyd.q4md-forcefieldtools.org>

Date: Sun, 05 Feb 2012 20:21:06 +0100

Thomas,

information about geometry constraints defined in the P2N file and

applied during geometry optimization - when using the Gaussian program

- only at R.E.D. Server or at R.E.D. Server Development; these pieces

of information are not yet written .

http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3 - to be

done...

regards, Francois

----- Forwarded message from fan.wang.q4md-forcefieldtools.org -----

Date: Fri, 16 Dec 2011 17:35:18 +0100

From: Fan Wang <fan.wang.q4md-forcefieldtools.org>

Reply-To: q4md-fft.q4md-forcefieldtools.org, Fan Wang

<fan.wang.q4md-forcefieldtools.org>

Subject: [q4md-fft] Constraint during geometry optimization

To: q4md-fft Mailing list <q4md-fft.q4md-forcefieldtools.org>

Cc: Francesco Pietra <francesco.pietra.accademialucchese.it>,

Francesco Pietra <chiendarret.gmail.com>, Albert

<mailmd2011.gmail.com>, "Crystal.CHIA-YU Ku"

<crystal.chia.yu.gmail.com>, Oliver Kuhn <oliver.kuhn.uni-due.de>,

ABEL Stephane 175950 <Stephane.ABEL.cea.fr>

Dear All,

The implementation of constraint(s) during geometry optimization is

now available in R.E.D. IV / R.E.D. Server

This new feature is limited to the interface of the Gaussian program,

so far; to be extended to the use of the GAMESS and Firefly programs.

Four types of constraints are handled in the P2N file format by using

the following formats:

- Cartesian coordinates can be constrained:

REMARK GEOM-OPT-CONSTRAINT W

- A bond between two atoms can be constrained:

REMARK GEOM-OPT-CONSTRAINT W X dst.val.

- An angle between three atoms can be constrained:

REMARK GEOM-OPT-CONSTRAINT W X Y agl.val.

- A dihedral angle between four atoms can be constrained:

REMARK GEOM-OPT-CONSTRAINT W X Y Z dhl.val.

* 'W', 'X', 'Y' and 'Z' are the atom numbers in the atom order of the

considered molecule

* dst.val. is the distance value between the two considered atoms in

Angstrom ( 0 < value >= 10)

* agl.val. is the angle value between the three considered atoms in

degrees ( 0 < value >= 180)

* dhl.val. is the dihedral value between the four considered atoms in

degrees (positive and negative values are handled)

Examples:

REMARK GEOM-OPT-CONSTRAINT 1

-> the Cartesian coordinates of the first atom in the atom order

are frozen.

REMARK GEOM-OPT-CONSTRAINT 1 2 1.5

-> the distance between the atoms one and two is set/frozen to 1.5

angstroms during geometry optimization

REMARK GEOM-OPT-CONSTRAINT 1 2 5 6 180

-> the dihedral angle between the four atoms 1 2 5 6 is set/frozen

to 180 degrees during geometry optimization

Example involving different conjugated constrains:

REMARK GEOM-OPT-CONSTRAINT 1

REMARK GEOM-OPT-CONSTRAINT 5

REMARK GEOM-OPT-CONSTRAINT 7

REMARK GEOM-OPT-CONSTRAINT 7 8 10 11 -60

Providing the right constraint value(s) for a bond, an angle and a

dihedral in the input geometry is strongly recommended.

This new feature is NOT yet documented at

http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3

(to be done)

regards, Fan

----- End forwarded message -----

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AMBER.ambermd.org

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Received on Sun Feb 05 2012 - 11:30:03 PST

Date: Sun, 05 Feb 2012 20:21:06 +0100

Thomas,

information about geometry constraints defined in the P2N file and

applied during geometry optimization - when using the Gaussian program

- only at R.E.D. Server or at R.E.D. Server Development; these pieces

of information are not yet written .

http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3 - to be

done...

regards, Francois

----- Forwarded message from fan.wang.q4md-forcefieldtools.org -----

Date: Fri, 16 Dec 2011 17:35:18 +0100

From: Fan Wang <fan.wang.q4md-forcefieldtools.org>

Reply-To: q4md-fft.q4md-forcefieldtools.org, Fan Wang

<fan.wang.q4md-forcefieldtools.org>

Subject: [q4md-fft] Constraint during geometry optimization

To: q4md-fft Mailing list <q4md-fft.q4md-forcefieldtools.org>

Cc: Francesco Pietra <francesco.pietra.accademialucchese.it>,

Francesco Pietra <chiendarret.gmail.com>, Albert

<mailmd2011.gmail.com>, "Crystal.CHIA-YU Ku"

<crystal.chia.yu.gmail.com>, Oliver Kuhn <oliver.kuhn.uni-due.de>,

ABEL Stephane 175950 <Stephane.ABEL.cea.fr>

Dear All,

The implementation of constraint(s) during geometry optimization is

now available in R.E.D. IV / R.E.D. Server

This new feature is limited to the interface of the Gaussian program,

so far; to be extended to the use of the GAMESS and Firefly programs.

Four types of constraints are handled in the P2N file format by using

the following formats:

- Cartesian coordinates can be constrained:

REMARK GEOM-OPT-CONSTRAINT W

- A bond between two atoms can be constrained:

REMARK GEOM-OPT-CONSTRAINT W X dst.val.

- An angle between three atoms can be constrained:

REMARK GEOM-OPT-CONSTRAINT W X Y agl.val.

- A dihedral angle between four atoms can be constrained:

REMARK GEOM-OPT-CONSTRAINT W X Y Z dhl.val.

* 'W', 'X', 'Y' and 'Z' are the atom numbers in the atom order of the

considered molecule

* dst.val. is the distance value between the two considered atoms in

Angstrom ( 0 < value >= 10)

* agl.val. is the angle value between the three considered atoms in

degrees ( 0 < value >= 180)

* dhl.val. is the dihedral value between the four considered atoms in

degrees (positive and negative values are handled)

Examples:

REMARK GEOM-OPT-CONSTRAINT 1

-> the Cartesian coordinates of the first atom in the atom order

are frozen.

REMARK GEOM-OPT-CONSTRAINT 1 2 1.5

-> the distance between the atoms one and two is set/frozen to 1.5

angstroms during geometry optimization

REMARK GEOM-OPT-CONSTRAINT 1 2 5 6 180

-> the dihedral angle between the four atoms 1 2 5 6 is set/frozen

to 180 degrees during geometry optimization

Example involving different conjugated constrains:

REMARK GEOM-OPT-CONSTRAINT 1

REMARK GEOM-OPT-CONSTRAINT 5

REMARK GEOM-OPT-CONSTRAINT 7

REMARK GEOM-OPT-CONSTRAINT 7 8 10 11 -60

Providing the right constraint value(s) for a bond, an angle and a

dihedral in the input geometry is strongly recommended.

This new feature is NOT yet documented at

http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3

(to be done)

regards, Fan

----- End forwarded message -----

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AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Sun Feb 05 2012 - 11:30:03 PST

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