From owner-nwchem-users@emsl.pnl.gov Wed Jul 9 21:02:11 2008 Received: from odyssey.emsl.pnl.gov (localhost.pnl.gov [127.0.0.1]) by odyssey.emsl.pnl.gov (8.14.1/8.14.1) with ESMTP id m6A42A4J001245 for ; Wed, 9 Jul 2008 21:02:11 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.14.1/8.14.1/Submit) id m6A42Ais001244 for nwchem-users-outgoing-0915; Wed, 9 Jul 2008 21:02:10 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Ironport-SG: Throttle X-Ironport-SBRS: 1.6 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AmcAAB8mdUjRVY68dGdsb2JhbACCc44/Y0MBDAMEBgcPBZZMhno X-IronPort-AV: E=Sophos;i="4.30,335,1212390000"; d="scan'208";a="55140809" DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:received:received:message-id:date:from:to :subject:cc:mime-version:content-type; bh=lXeXenv8BwN1wVMPrJGYqyHRZaVHoj+f/vNMVyEtiPg=; b=T0zbbcgzXC3I7kkBtWZm18dKIPQi05FK5DYO8SpLVgWduX5mhAz9qlxV4/beM5fNgZ 6Iji7RNLKJS5teOryZ+nczSkTBY++d0U/ACu5yM8Uk+Fh+IfKbH2cjBVwQdVjHrmhuWs q7POwTx3VN9HM9gB8tcKWwHxadZRQRmYbxodc= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=message-id:date:from:to:subject:cc:mime-version:content-type; b=Csk+SRUMRkil7sumS3+d9xa2xwFwG7rBjC/+1//+xaZGpnDCyga/X5/KsKs7yV2n95 Dy3nu2ZlOKQgHAb84A2DLLwU3uUIPGqHq1sDZq/gDc1+WIv0d/N6l49aLb3xc6D60tYK yUHmKo6SLczhLlCI7w2Ye6Y45yzlZNaK9j+eo= Message-ID: Date: Wed, 9 Jul 2008 23:02:03 -0500 From: "shiyu du" To: nwchem-users@emsl.pnl.gov Subject: [NWCHEM] geometry constraints of a CPMD Cc: dushiyu@gmail.com MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_10596_19294909.1215662523328" Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk ------=_Part_10596_19294909.1215662523328 Content-Type: text/plain; charset=WINDOWS-1252 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi, all, I am trying to do a Car=96Parrinello molecular dynamics simulation for a system containg 4 H2O molecule and 2 OH radical. I hope to freeze the coordinates for the O atoms in the four water molecule= . So I used the following input. geometry units angstroms nocenter noautosym noautoz print xyz O 1.55791800 -0.08009500 -0.10253600 H 1.45401000 -0.71050100 0.62496300 H 0.65990900 -0.04094500 -0.48844200 O -1.30124400 -0.01160300 -0.19786500 H -1.32065400 0.75220400 0.39700000 H -2.23071900 -0.09987000 -0.48679800 O -4.15671700 0.01314100 -0.38290900 H -4.49342200 -0.76663000 0.12483000 H -4.70367800 -0.00543000 -1.18763200 O -7.00489600 -0.00260500 -0.65897400 H -6.80374400 0.81423900 -0.14342600 H -7.92652100 0.07673300 -0.94802900 O -5.76817100 -1.92449800 0.79699500 H -6.45616800 -1.36347100 0.33005900 O -5.69907400 2.00081100 0.72762000 H -4.94200600 1.40973100 0.43603300 end pspw Car-Parrinello time_step 5.0 loop 10 10000 xyz_filename lw12s_con01.xyz xc pbe96 end odft xc pbe96 lmbfgs cutoff 30.0 MULT 1 end set geometry:actlist 2 3 5 6 8 9 11 12 13 14 15 16 task pspw energy task pspw Car-Parrinello set nwpw:com_shift .false. The Label for the four O atoms in H2O molecules are 1, 4, 7, 10 respectively. So I didn't put them in the "actlist". I expect this MD simulation will run with the four O atoms freezing. However, after calculation is done, I found the O atoms all moves in the trajectory file 'lw12s_con01.xyz"!!!!! Can some one help me finding out what I should correct my input file to freeze the O atoms in water molecules? Thanks a lot. ------=_Part_10596_19294909.1215662523328 Content-Type: text/html; charset=WINDOWS-1252 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
 
Hi, all,
 
I am trying to do a Car=96Parrinello molecular dynamics simulation for= a system containg 4 H2O molecule and 2 OH radical.
 
I hope to freeze the coordinates for the O atoms in the four water mol= ecule. So I used the following input.
 

geometry  units angstroms nocenter noautosym noautoz print xyz
&= nbsp;O           &nb= sp;      1.55791800   -0.08009500 &= nbsp; -0.10253600
 H        = ;          1.45401000 &nb= sp; -0.71050100    0.62496300
 H   &n= bsp;            = ;  0.65990900   -0.04094500   -0.48844200
 O           &n= bsp;     -1.30124400   -0.01160300  = ; -0.19786500
 H        &nb= sp;        -1.32065400   = 0.75220400    0.39700000
 H    =              -2= .23071900   -0.09987000   -0.48679800
 O &= nbsp;           &nbs= p;   -4.15671700    0.01314100   -0.3829= 0900
 H           &n= bsp;     -4.49342200   -0.76663000  = ;  0.12483000
 H       &nbs= p;         -4.70367800   = -0.00543000   -1.18763200
 O     = ;            -7.0048= 9600   -0.00260500   -0.65897400
 H  =             &nb= sp;  -6.80374400    0.81423900   -0.14342600<= br>  H           &n= bsp;     -7.92652100    0.07673300 =   -0.94802900
 O       &nbs= p;         -5.76817100   = -1.92449800    0.79699500
 H    =              -6= .45616800   -1.36347100    0.33005900
 O&n= bsp;            = ;    -5.69907400    2.00081100  &nb= sp; 0.72762000
 H           &n= bsp;     -4.94200600    1.40973100 =    0.43603300
end

pspw
  Car-Parrinello
     time_step 5.0<= br>     loop 10 10000
     xyz_f= ilename lw12s_con01.xyz
     xc pbe96
  end<= br>  odft
  xc pbe96
  lmbfgs
  cutoff 30.0   MULT 1
end
 set geometry:actlist 2 3 5 6 8 9 11 12 13 1= 4 15 16
task pspw energy
task pspw Car-Parrinello
set nwpw:com_shift .false.<= /p>

The Label for the four O atoms in H2O molecules are 1, 4, 7, 10 respecti= vely. So I didn't put them in the "actlist". I expect this MD= simulation will run with the four O atoms freezing.

However, after calculation is done, I found the O atoms all moves in the= trajectory file 'lw12s_con01.xyz"!!!!!

Can some one help me finding out what I should correct my input fil= e to freeze the O atoms in water molecules?

Thanks a lot. 

 

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