From owner-nwchem-users@emsl.pnl.gov Fri Jul 13 10:23:49 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 l6DHNmAT002042 for ; Fri, 13 Jul 2007 10:23:49 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id l6DHNmJA002041 for nwchem-users-outgoing-0915; Fri, 13 Jul 2007 10:23:48 -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="4.16,537,1175497200"; d="scan'208,217";a="39253113" 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_01C7C572.914D053A" Subject: RE: [NWCHEM] Quantum MD geometry input Date: Fri, 13 Jul 2007 10:23:45 -0700 Message-ID: <37275E1A43F1EC4C938AEFA1CFFAA0E301A5F551@EMAIL02.pnl.gov> In-Reply-To: <6DE4A14FA13FF74E9C6D9A9501FCEB461CFE0C@stumbx.wittenberg.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: [NWCHEM] Quantum MD geometry input Thread-Index: AQHHxV0RyWE/+pPnQ0W3oxQdbl6HXIv7WS8Q References: <6DE4A14FA13FF74E9C6D9A9501FCEB461CFE0C@stumbx.wittenberg.edu> From: "Vorpagel, Erich R" To: "Joseph Fritchman" Cc: X-OriginalArrivalTime: 13 Jul 2007 17:23:46.0534 (UTC) FILETIME=[91BC7860:01C7C572] Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk This is a multi-part message in MIME format. ------_=_NextPart_001_01C7C572.914D053A Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Greetings Joe, =20 To run QMD in NWChem the molecular coordinates must be entered into the "geometry" input block. For classical MD the geometry must be entered as a pdb file. To start QMD from a pdb file, you will need to cut&paste the element and coordinate information into the geometry block of the input file. =20 =20 Or if you have ECCE, you can read in the pdb file and submit the calculation as an electronic structure calculation. But from ECCE you will need to edit the input file using "Final Edit" to add the MD input block and task. =20 Regards, =20 Erich R. Vorpagel, Ph.D. Technical Group Leader=20 Manager Computational Grand-Challenge and Pilot Projects=20 MSCF Visualization and User Services Group=20 Environmental Molecular Sciences Laboratory=20 Pacific Northwest National Laboratory =20 P. O. Box 999, MS: K8-91=20 3335 Q Ave. Phone: 509-376-0751=20 Richland, WA 99352 FAX: 509-376-0420=20 Email: erich.vorpagel@pnl.gov=20 Web: http://mscf.emsl.pnl.gov/=20 ________________________________ From: owner-nwchem-users@emsl.pnl.gov [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of Joseph Fritchman Sent: Friday, July 13, 2007 7:50 AM To: nwchem-users@emsl.pnl.gov Subject: [NWCHEM] Quantum MD geometry input Hi, =20 I am running quantum MD simulations and am only able to run using a starting geometry from the runtime database. When I try using the prepare module loading a .pdb file, I receive the following error. =20 geom_rtdb_load failed::=20 =20 Classical MD seems to work the opposite way in that it works using .pdb input but not input into the geometry module. Is there a way to run QMD from a starting geometry in a .pdb file? =20 Thank you, -Joe Fritchman ------_=_NextPart_001_01C7C572.914D053A Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Greetings Joe,

To run QMD in NWChem the molecular coordinates = must be=20 entered into the "geometry" input block. For classical MD the = geometry=20 must be entered as a pdb file. To start QMD from a pdb file, you = will need=20 to cut&paste the element and coordinate information into the = geometry block=20 of the input file.

Or if you have ECCE, you can read in the pdb = file and=20 submit the calculation as an electronic structure calculation. But = from=20 ECCE you will need to edit the input file using "Final Edit" to add the = MD input=20 block and task.

Regards,

Erich R. Vorpagel,=20 Ph.D.      Technical Group = Leader=20
Manager = Computational=20 Grand-Challenge and Pilot Projects
MSCF Visualization and User Services Group=20
Environmental=20 Molecular Sciences Laboratory
Pacific Northwest National Laboratory =20
P. O. = Box 999, =20 MS: K8-91
3335 Q=20 Ave.           &nb= sp;           &nbs= p;         =20 Phone: 509-376-0751
Richland, WA =20 99352           &n= bsp;        =20 FAX:      509-376-0420
Email: erich.vorpagel@pnl.gov=20
Web: http://mscf.emsl.pnl.gov/=20

From: = owner-nwchem-users@emsl.pnl.gov=20 [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of Joseph=20 Fritchman
Sent: Friday, July 13, 2007 7:50 AM
To:=20 nwchem-users@emsl.pnl.gov
Subject: [NWCHEM] Quantum MD = geometry=20 input

Hi,

I am running quantum MD = simulations=20 and am only able to run using a starting geometry from the runtime=20 database. When I try using the prepare module loading a .pdb file, = I=20 receive the following error.

geom_rtdb_load failed::

Classical MD seems to work = the=20 opposite way in that it works using .pdb input but not input into the = geometry=20 module. Is there a way to run QMD from a starting geometry in a = .pdb=20 file?

Thank you,

-Joe=20 Fritchman

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