From owner-nwchem-users@emsl.pnl.gov Fri Jul 6 15:29:41 2007 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.8/8.13.8) with ESMTP id l66MTd2V007560 for ; Fri, 6 Jul 2007 15:29:40 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id l66MTdN8007559 for nwchem-users-outgoing-0915; Fri, 6 Jul 2007 15:29:39 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Possible-Spoof: True X-IronPort-AV: E=Sophos;i="4.16,510,1175497200"; d="scan'208,217";a="38445706" X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7C01D.22A64726" Subject: RE: [NWCHEM] QM/MM geometry constraints Date: Fri, 6 Jul 2007 15:29:36 -0700 Message-ID: <9EA84B4DE79CD74F89F814624913B70503AA1909@EMAIL01.pnl.gov> In-Reply-To: <59F8E9364A4B184EA893B98611CFC88E01617117@XMAIL.ds.utpa.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: [NWCHEM] QM/MM geometry constraints Thread-index: Ace/RK/2KaZpMPi6R/K69k27HfzfFwAqMNKAAATyoukABpzu4A== References: <59F8E9364A4B184EA893B98611CFC88E01617113@XMAIL.ds.utpa.edu> <9EA84B4DE79CD74F89F814624913B70503AA180E@EMAIL01.pnl.gov> <59F8E9364A4B184EA893B98611CFC88E01617117@XMAIL.ds.utpa.edu> From: "Valiev, Marat" To: "Mark Cunningham" Cc: X-OriginalArrivalTime: 06 Jul 2007 22:29:37.0350 (UTC) FILETIME=[22C88660:01C7C01D] Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk This is a multi-part message in MIME format. ------_=_NextPart_001_01C7C01D.22A64726 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear Mark, =20 Internally NWChem uses Cartesian geometry, as does QM/MM code. The best way to constrain the distance between atoms is to use constraint module where one can put a spring between two atoms. The indexing is that of QM geometry. The best way to get it is to run single point energy and look either in the input file or *active.pdb file.=20 =20 Here is an example. Let me know if it does not work. =20 ---------- =20 memory total 2000 Mb start clfoh permanent_dir ./perm scratch_dir /scratch =20 charge -1 =20 basis "ao basis" * library "6-31+G*" end =20 dft print low XC b3lyp iterations 5000 end =20 task shell "cp clfoh_ps00.rst clfoh_rs00.rst" md system clfoh_rs00 cutoff 1.5 qmmm 1.5 noshake solute end =20 constraints fix atom 7 fix atom 6 fix atom 1 spring bond 1 5 3.0 1.89 end =20 qmmm region qm solvent method bfgs sd xyz rs maxiter 30 3000 density espfit ncycles 20 end =20 task qmmm dft optimize =20 Marat Valiev, Ph.D. Senior Research Scientist Molecular Sciences Software Group (NWChem) marat.valiev@pnl.gov =20 From: Mark Cunningham [mailto:cunningham@utpa.edu]=20 Sent: Friday, July 06, 2007 12:18 PM To: Valiev, Marat Subject: RE: [NWCHEM] QM/MM geometry constraints =20 Dr. Valiev: =20 I am interested in constraining the distance between two atoms in the quantum partition. Must I place an harmonic restraint on the=20 atoms? =20 =20 I thought that the QM/MM code invoked the standard QM utilities to compute energies and the like and that NWChem used internal coordinate representations internally. Is there some way to (manually) force an internal coordinate in the QM part of a QM/MM calculation? I could/would modify the appropriate code if you can point me in the proper direction. =20 Thanks for your help =20 Mark Cunningham =20 ________________________________ From: Valiev, Marat [mailto:marat.valiev@pnl.gov] Sent: Fri 7/6/2007 11:49 AM To: Mark Cunningham; nwchem-users@emsl.pnl.gov Subject: RE: [NWCHEM] QM/MM geometry constraints Mark, =20 QM/MM module does not use internal coordinates representation, thus your errors. Also aside the potential use, the actual charmm fragment files have never been tested. I would recommend using AMBER force field. =20 Marat Valiev, Ph.D. Senior Research Scientist Molecular Sciences Software Group (NWChem) marat.valiev@pnl.gov =20 From: owner-nwchem-users@emsl.pnl.gov [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of Mark Cunningham Sent: Thursday, July 05, 2007 1:40 PM To: nwchem-users@emsl.pnl.gov Subject: [NWCHEM] QM/MM geometry constraints =20 I am trying to use NWChem 5.0 to perform QM/MM calculations but my progress has been hampered by the fact that none of the examples in the distribution actually run. Additionally, it appears that all of the CHARMM fragment files are incorrect. =20 My problem at the moment is to specify a geometry constraint. In an all QM calculation, I can use zcoord to force an atom-atom distance to be some value without having to use an harmonic restraint. In a QM/MM calculation, I tried using=20 the same strategy: after task prepare, I specified: =20 geometry zcoord bond 77 153 3.5 constant torsion 69 71 77 153 178.12 constant end end This results in the following error: User specification of redundant internal variables -------------------------------------------------- i j k l value name frz --- --- --- --- ------------ -------- --- 77 153 3.500000 User001 T 69 71 77 153 178.120000 User002 T Scaling coordinates for geometry "geometry" by 1.889725989 (inverse scale =3D 0.529177249) geom_cart_set: too many centers 0 geometry geom_masses_set: too many centers 0 geometry geom_nucexps_set: too many centers 0 geometry =20 ------------------------------------------------------------------------ geom_input: geom_nucexps_set failed 0 =20 ------------------------------------------------------------------------ =20 ------------------------------------------------------------------------ current input line : 42: end =20 ------------------------------------------------------------------------ I would appreciate any advice. =20 Mark A Cunningham The University of Texas-Pan American =20 ------_=_NextPart_001_01C7C01D.22A64726 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear Mark,

 

Internally NWChem uses Cartesian geometry, as does QM/MM = code.

The best way to constrain the distance between atoms is to = use constraint module

where one can put a spring between two atoms. The indexing = is that of QM geometry. The best way to get it is to run

single point energy and look either in the input file or *active.pdb file.

 

Here is an example. Let me know if it does not = work.

 

----------

 

memory total 2000 Mb

start clfoh

permanent_dir  ./perm

scratch_dir /scratch

 

charge -1

 

basis "ao basis"

 * library "6-31+G*"

end

 

dft

print low

XC b3lyp

iterations 5000

end

 

task shell "cp clfoh_ps00.rst = clfoh_rs00.rst"

md

 system clfoh_rs00

 cutoff 1.5 qmmm 1.5

 noshake solute

end

 

constraints

fix atom 7

fix atom 6

fix atom 1

spring bond 1 5  3.0 1.89

end

 

qmmm

region qm solvent

method bfgs sd

xyz    rs

maxiter 30 3000

density espfit

ncycles 20

end

 

task qmmm dft optimize

 

Marat = Valiev, Ph.D.
Senior Research Scientist
Molecular Sciences Software Group (NWChem)
marat.valiev@pnl.gov
 

From:= Mark = Cunningham [mailto:cunningham@utpa.edu]
Sent: Friday, July 06, 2007 12:18 PM
To: Valiev, Marat
Subject: RE: [NWCHEM] QM/MM geometry = constraints

 

Dr. Valiev:

 

I am interested in constraining the distance between two atoms = in

the quantum partition.  Must I place an harmonic restraint on the =

atoms? 

 

I thought that the QM/MM code invoked the standard

QM utilities to compute energies and the like and that = NWChem

used internal coordinate representations internally.  Is = there

some way to (manually) force an internal coordinate in = the

QM part of a QM/MM calculation?  I could/would modify = the

appropriate code if you can point me in the proper direction.

 

Thanks for your help

 

Mark Cunningham

 

From: Valiev, Marat = [mailto:marat.valiev@pnl.gov]
Sent: Fri 7/6/2007 11:49 AM
To: Mark Cunningham; nwchem-users@emsl.pnl.gov
Subject: RE: [NWCHEM] QM/MM geometry = constraints

Mark,

 

QM/MM module does not use internal coordinates = representation, thus your errors.

Also aside the potential use, the actual charmm fragment = files have never been tested.

I would recommend using AMBER force = field.

 

Marat Valiev, Ph.D.
Senior Research Scientist
Molecular Sciences Software Group (NWChem)
marat.valiev@pnl.gov

 

From:= owner-nwchem-users@emsl.pnl.gov [mailto:owner-nwchem-users@emsl.pnl.gov] = On Behalf Of Mark Cunningham
Sent: Thursday, July 05, 2007 1:40 PM
To: nwchem-users@emsl.pnl.gov
Subject: [NWCHEM] QM/MM geometry = constraints

 

I am trying to use NWChem 5.0 to perform QM/MM calculations = but my progress

has been hampered by the fact that none of the examples in the = distribution

actually run.  Additionally, it appears that all of the CHARMM fragment = files are

incorrect.

 

My problem at the moment is to specify a geometry constraint.  In an = all QM

calculation, I can use zcoord to force an atom-atom distance to be some = value

without having to use an harmonic restraint.  In a QM/MM calculation, = I tried using

the same strategy: after task prepare, I specified:

 

geometry
   zcoord
      bond 77 153 3.5 constant
      torsion 69 71 77 153 178.12 constant
   end
end

This results in the following error:

User = specification of redundant internal variables
 --------------------------------------------------

   i   j   k   l     value       name   frz
  --- --- --- --- ------------ -------- ---
   77 153           &nbs= p; 3.500000 User001    T
   69  71  77 153   178.120000 User002    T


 Scaling coordinates for geometry "geometry" by  1.889725989
 (inverse scale =3D  0.529177249)

  geom_cart_set: too many centers           =            0 geometry
  geom_masses_set: too many centers           =            0 geometry
  geom_nucexps_set: too many centers           =            0 geometry
 -------------------------------------------------------------------= -----
 geom_input: geom_nucexps_set failed        0
 -------------------------------------------------------------------= -----
 -------------------------------------------------------------------= -----
  current input line :
    42: end
 -------------------------------------------------------------------= -----

I would appreciate any advice.

 

Mark A Cunningham

The University of Texas-Pan American

 

------_=_NextPart_001_01C7C01D.22A64726--