From owner-nwchem-users@emsl.pnl.gov Mon Mar 27 06:42:43 2006 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.6/8.13.6) with ESMTP id k2REghmH015080 for ; Mon, 27 Mar 2006 06:42:43 -0800 (PST) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.6/8.13.6/Submit) id k2REghNB015079 for nwchem-users-outgoing-0915; Mon, 27 Mar 2006 06:42:43 -0800 (PST) Date: Mon, 27 Mar 2006 09:38:53 -0500 From: JunJun Liu Subject: Re: [NWCHEM] about defining quantum atoms In-reply-to: To: "Vorpagel, Erich R" , nwchem-users@emsl.pnl.gov Message-id: MIME-version: 1.0 Content-type: text/plain; format=flowed; delsp=yes; charset=utf-8 Content-transfer-encoding: 8bit DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:date:to:subject:from:content-type:mime-version:references:content-transfer-encoding:message-id:in-reply-to:user-agent; b=aN3BPJKg+Tq/Om71gJc9Qg/tMNB1b8qnTPMjLPDL1xKp71sbzBQ+2SqFatFNPxXrw7S+xsUpFEgbNh14fKiMvp5tgrlskVbL6mAmMbqd8YPNFV6+4nXyvIQSyWQTzTawqqtSDybQ9DA3JKjubKU8m8r+7z7BrzIu9N53k3ZbGkY= User-Agent: Opera Mail/9.00 (Linux) References: Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Dear Dr.Vorpagel Thanks a lot for your response! I've managed redeclaring the solvent to solute. Since the description in manual for file format does not match the latest file, could you please tell me where I can find the correct file format description for the latest file? Or could your please be so kind sending me the latest file format description? Some fragment files that NWChem4.7 generated lost something and thus need revision, so I want to know the format to ensure my modification is correct. Thanks! Best Regards! Liu On Mon, 27 Mar 2006 01:33:37 -0500, Vorpagel, Erich R wrote: > Greetings Liu, > > The fragment and segment formats described in the 4.7 version of NWChem > actually are formats for versions prior to 4.6. They will be updated in > the next release. If you want to have a water molecule treated quantum > mechanically, make a copy of the HOH.frg and call it WAT.frg Inside the > new WAT.frg, change all occurrences of HOH to WAT. Then in the PDB > file, make sure the residue name for the QM water molecules are changed > from HOH to WAT. > > REMEMBER: ALL FILES are COLUMN sensitive. Good ol' 80 character per > card FORTRAN. > > Regards, > > Erich R. Vorpagel Ph.D. Chief Scientist > Manager of Computational Grand Challenge and Pilot Projects > MSCF Visualization and User Services Group > Environmental Molecular Sciences Laboratory > Pacific Northwest National Laboratory > P. O. Box 999, MS: K8-91 > 3335 Q Ave. Phone: 509-376-0751 > Richland, WA 99352 FAX: 509-376-0420 > Web: http://mscf.emsl.pnl.gov/ > > > > -----Original Message----- > From: owner-nwchem-users@emsl.pnl.gov > [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of JunJun Liu > Sent: Sunday, March 26, 2006 5:41 PM > To: Valiev, Marat; nwchem-users@emsl.pnl.gov > Subject: Re: [NWCHEM] about defining quantum atoms > > Hi, Marat > > I got it, thank you very much! But now I have another question > concerning the format of fragment. By taking the > $NWCHEM_TOP/src/data/amber_s/ACE.frg > as an example, the first 4 lines are as followed: > -------- > $ACE > 6 1 1 0 > ACE > 12HH3 HC 0 0 0 1 1 0.112300 0.000000 > --------- > My question is: > 1). The second line(" 6 1 1 0") contains 4 digitals. But the > > manual where describing the format of fragment files(page 276) only > explains the meaning of the first digital. What do the other 3 digitals > stand for? > 2). According to the manul, in the 4th line of the above example, the > field after "HC"(atom type), should be dynamics type with the fortran > format "a1", which should be a character. But here it's a digital "0" > > I also notice the output of the program give different description(see > below) for the fragment file: > ----- > num name type link cntr grp pgrp charge polarizab > 2 H1 HO 0 0 0 1 1 0.000000 0.000000 > ----- > Maybe this is more correct. However, the description line only contains > 9 fields whilas the data for each atom has 10 fields. This confuse me > that what do each field really stand for. > > Could you please explain this for me? Thanks in advance! > > > Regards! > > Liu > > On Sun, 26 Mar 2006 19:15:41 -0500, Valiev, Marat > wrote: > >> By default all waters bearing residue name HOH will be classified as >> solvent. If some waters are to be declared quantum their name should >> be changed to something other than HOH. Whatever naming you choose >> make sure to create matching fragment or segment file. There are many >> example fragment files in the amber_s directory. >> >> >> ************ >> Marat Valiev >> Molecular Sciences Software Group (NWChem) EMSL, MSIN: K8-91 >> Phone: (509) 376-2514 >> Fax: (509)376-0420 >> email: marat.valiev@pnl.gov >> *************************** >> >> -----Original Message----- >> From: owner-nwchem-developers@emsl.pnl.gov >> [mailto:owner-nwchem-developers@emsl.pnl.gov] On Behalf Of JunJun Liu >> Sent: Sunday, March 26, 2006 3:38 PM >> To: nwchem-users@emsl.pnl.gov >> Subject: [NWCHEM] about defining quantum atoms >> >> Hello everyone, >> >> I'm reading QM/MM on the NWChem4.7 mannual and having a question right > >> now. I hope anyone who knows the answer can kindly tell me. Thanks in >> advance! >> >> On the page 270, The following statement is printed: >> "In the current implementation only solute atoms can be declared as >> quantum. If part of the solvent has to be treated quantum mechanically > >> then it has to redeclared to be solute." >> >> My question is: >> 1). How does NWChem recognize the atom to be of solute or solvent? Is >> it true that all atoms in PDB file are treated as solute? Or are atoms > >> recognized according to the atom/residue name? >> 2). If I want to redeclare a solvent to be a solute, how to do? >> >> Any help/advice is highly appreciated! >> >> Best Regards! -- JunJun Liu College of Chemistry Central China Normal University WuHan 430079 P.R. China