From owner-nwchem-users@emsl.pnl.gov Wed Nov 15 12:21:54 2006 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 kAFKLrQP026151 for ; Wed, 15 Nov 2006 12:21:54 -0800 (PST) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id kAFKLrCH026150 for nwchem-users-outgoing-0915; Wed, 15 Nov 2006 12:21:53 -0800 (PST) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-IronPort-AV: i="4.09,425,1157353200"; d="scan'208"; a="8218232:sNHT41009024" X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Subject: RE: [NWCHEM] question about topology file and "error on integrated density" Date: Wed, 15 Nov 2006 12:21:50 -0800 Message-ID: <9EA84B4DE79CD74F89F814624913B705A0CD1C@EMAIL01.pnl.gov> In-Reply-To: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: [NWCHEM] question about topology file and "error on integrated density" Thread-Index: AccI8K4e7ECr2xDCQWOTWxYMd+pf6AAACFTw From: "Valiev, Marat" To: "JunJun Liu" , X-OriginalArrivalTime: 15 Nov 2006 20:21:51.0049 (UTC) FILETIME=[AF101390:01C708F3] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by odyssey.emsl.pnl.gov id kAFKLq5C026147 Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk 1) Topology has no coordinate information, just the parameters of interaction that will be affected if QM region definition was changed. In your case and 99.9% of all QM/MM calculations topology file should remain the same for a given reaction process 2) Convergence of DFT part of calculations depends on many factors and may sometime take few iterations. I do not see anything particularly wrong with your output here. Marat Valiev, Ph.D. Senior Research Scientist Molecular Sciences Software Group (NWChem) marat.valiev@pnl.gov -----Original Message----- From: owner-nwchem-users@emsl.pnl.gov [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of JunJun Liu Sent: Wednesday, November 15, 2006 11:42 AM To: nwchem-users@emsl.pnl.gov Subject: [NWCHEM] question about topology file and "error on integrated density" Dear sir, Now I am doing QM/MM calculation with NWChem. I am studying an enzymatic reaction pathways and I have found some intermediates and transition state. I have two questions: (1) If the QM and MM region selected are the same for those intermediates and transition states, whether should their topology file be the same as each other? Could you please me tell me the meaning of every data in topology file? (2) I am doing single point energy calculation for QM/MM system, but the results are as follows: whether does the result show that it can't be converged for this single point energy calculation? d= 0,ls=0.5,diis 73 -4733.8015833553 -2.33D-04 2.82D-03 2.69D-03 69958.5 Bq nuclear interaction energy is -243.751065703780 WARNING: error on integrated density = 0.15D-05 greater than required accuracy of 0.10D-05 d= 0,ls=0.5,diis 74 -4733.8017876139 -2.04D-04 3.55D-03 2.91D-03 70916.1 Bq nuclear interaction energy is -243.751065703780 WARNING: error on integrated density = 0.15D-05 greater than required accuracy of 0.10D-05 d= 0,ls=0.5,diis 75 -4733.8019684659 -1.81D-04 2.85D-03 3.39D-03 71870.3 Bq nuclear interaction energy is -243.751065703780 WARNING: error on integrated density = 0.15D-05 greater than required accuracy of 0.10D-05 d= 0,ls=0.5,diis 76 -4733.8021733442 -2.05D-04 1.16D-03 3.46D-03 72821.9 Bq nuclear interaction energy is -243.751065703780 WARNING: error on integrated density = 0.15D-05 greater than required accuracy of 0.10D-05 d= 0,ls=0.5,diis 77 -4733.8023856860 -2.12D-04 2.19D-03 3.25D-03 73778.0 Bq nuclear interaction energy is -243.751065703780 -- JunJun Liu College of Chemistry Central China Normal University WuHan 430079 P.R. China