Custom Search
-- Asim Okur Stony Brook University Chemisty Department Stony Brook, NY 11794-3400 631 - 632 1560 ygao.phase1.unl.edu wrote: >Now the output is > >File Assignments: >| MDIN: min.in >| MDOUT: min.out >|INPCRD: hepta-water.crd >| PARM: hepta-water.top >|RESTRT: hepta-water.rst >| REFC: refc >| MDVEL: mdvel >| MDEN: mden >| MDCRD: mdcrd >|MDINFO: mdinfo >|INPDIP: inpdip >|RSTDIP: rstdip > > > Here is the input file: > > &cntrl > imin=1,maxcyc=100, > nptr=1, > / > > > > Could not find cntrl namelist > > >Thanks! > >Yi > > >On Thu, 20 Jan 2005, Ross Walker wrote: > > > >>Use the following input file: >> >>molecular dynamics run >> &cntrl >> imin=1,maxcyc=100, >> ntpr=1, >> / >> >>Then let me know what the error is, if there is one. >> >>All the best >>Ross >> >>/\ >>\/ >>|\oss Walker >> >>| Department of Molecular Biology TPC15 | >>| The Scripps Research Institute | >>| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk | >>| http://www.rosswalker.co.uk/ | PGP Key available on request | >> >>Note: Electronic Mail is not secure, has no guarantee of delivery, may not >>be read every day, and should not be used for urgent or sensitive issues. >> >> >> >> >>>-----Original Message----- >>>From: owner-amber.scripps.edu >>>[mailto:owner-amber.scripps.edu] On Behalf Of ygao.phase1.unl.edu >>>Sent: 20 January 2005 14:10 >>>To: amber.scripps.edu >>>Subject: RE: AMBER: sander failure >>> >>>Thanks for your reply.But it looks like the program never >>>launch at all. >>>The output file is as follows: >>> >>> ------------------------------------------------------- >>> Amber 8 SANDER Scripps/UCSF 2004 >>> ------------------------------------------------------- >>> >>>| Run on 01/20/2005 at 16:12:46 >>> [-O]verwriting output >>> >>>File Assignments: >>>| MDIN: min.in >>>| MDOUT: min.out >>>|INPCRD: hepta-water.crd >>>| PARM: hepta-water.top >>>|RESTRT: hepta-water.rst >>>| REFC: refc >>>| MDVEL: mdvel >>>| MDEN: mden >>>| MDCRD: mdcrd >>>|MDINFO: mdinfo >>>|INPDIP: inpdip >>>|RSTDIP: rstdip >>> >>> >>> Here is the input file: >>> >>>molecular dynamics run >>> &cntrl >>> imin=1,maxcyc=100, >>> nptr=1, >>> &end >>>END >>> >>> >>>I've only launched it on single CPU, but get the same errors. >>> >>>Yi >>> >>> >>>On Thu, 20 Jan 2005, Ross Walker wrote: >>> >>> >>> >>>>Dear Yi, >>>> >>>> >>>> >>>>>molecular dynamics run >>>>> &cntrl >>>>> imin=1,maxcyc=100, >>>>> nptr=10, >>>>> &end >>>>>END >>>>> >>>>> >>>>Change nptr to ntpr and try again... >>>> >>>>Note: It is often best to test out your job on a single cpu >>>> >>>> >>>first to ensure >>> >>> >>>>it works before running it in parallel. Error messages are >>>> >>>> >>>often more vague, >>> >>> >>>>or lost all together when running in parallel. >>>> >>>>All the best >>>>Ross >>>> >>>>/\ >>>>\/ >>>>|\oss Walker >>>> >>>>| Department of Molecular Biology TPC15 | >>>>| The Scripps Research Institute | >>>>| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk | >>>>| http://www.rosswalker.co.uk/ | PGP Key available on request | >>>> >>>>Note: Electronic Mail is not secure, has no guarantee of >>>> >>>> >>>delivery, may not >>> >>> >>>>be read every day, and should not be used for urgent or >>>> >>>> >>>sensitive issues. >>> >>> >>>> >>>> >>>-------------------------------------------------------------- >>>--------- >>> >>> >>>>The AMBER Mail Reflector >>>>To post, send mail to amber.scripps.edu >>>>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu >>>> >>>> >>>> >>>__________________________________________________________ >>> >>>Department of Chemistry >>>University of Nebraska -- Lincoln >>>Lincoln, NE, USA 68508 >>> >>>Phone: 1-402-472-9982 (O) >>> 1-402-310-4155 (M) >>>Email: ygao.phase1.unl.edu >>> >>>__________________________________________________________ >>>-------------------------------------------------------------- >>>--------- >>>The AMBER Mail Reflector >>>To post, send mail to amber.scripps.edu >>>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu >>> >>> >>> >>----------------------------------------------------------------------- >>The AMBER Mail Reflector >>To post, send mail to amber.scripps.edu >>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu >> >> >> > >__________________________________________________________ > >Department of Chemistry >University of Nebraska -- Lincoln >Lincoln, NE, USA 68508 > >Phone: 1-402-472-9982 (O) > 1-402-310-4155 (M) >Email: ygao.phase1.unl.edu > >__________________________________________________________ >----------------------------------------------------------------------- >The AMBER Mail Reflector >To post, send mail to amber.scripps.edu >To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > > ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Thu Jan 20 2005 - 22:53:00 PST