[gmx-users] AMBER force constants into GROMOS-96 units
David
spoel at xray.bmc.uu.se
Thu Nov 17 19:19:55 CET 2005
On Thu, 2005-11-17 at 09:52 -0800, chandran karunakaran wrote:
> Dear GMX users
>
> I am interested in doing of MD of plastocyanin using
> GROMOS-96 force field. But I have bond length's
> force
> constant only in AMBER.
>
> Now I need force constant in Gromos-96 units. So,
> could
> you please help to convert Amber force constant into
> Gromo-96
> force constant OR give the CU-N , CU-S FORCE CONSTANT
> IN
> gromos-96 units which is in KJ/MOL NM*4 .
ch. 4 in the manual
>
> Thanks in advance for your help.
>
> With thanks
> Dr.C.Karunakaran
>
>
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> > Today's Topics:
> >
> > 1. Re: CFLAGS (Florian Haberl)
> > 2. order parameter per slice
> > (paloureiro at biof.ufrj.br)
> > 3. list of protein parameters/ properties (gaurav
> > gupta)
> > 4. Re: CFLAGS (Joanne Hanna)
> > 5. Re: Handling of charge field in PDB files by
> > x2top
> > (Nathan C. Rockwell)
> > 6. RE: Isobaric - isothermal ensemble and Replica
> > Exchange
> > (Luca Mollica)
> > 7. -t and -shuffle problem in grompp (Eric
> > Carpenter)
> >
> >
> >
> ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 16 Nov 2005 18:04:49 +0100
> > From: Florian Haberl
> > <Florian.Haberl at chemie.uni-erlangen.de>
> > Subject: Re: [gmx-users] CFLAGS
> > To: Discussion list for GROMACS users
> > <gmx-users at gromacs.org>
> > Message-ID: <200511161804.49897.haberl at scotty>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > hi,
> >
> > On Wednesday 16 November 2005 17:47, Joanne Hanna
> > wrote:
> > > Hi
> > >
> > > So if my machine is Intel Itanium2 should i really
> > use version 3.3? and if
> > > i use 3.2.1 should i use the -O3 cflags option?
> > Sorry I am quite new to
> > > compiling!
> >
> > Normally you don^t use optimazition flags for
> > compiling gromacs, only if you
> > want to test further improvement of the speed, as
> > Erik Lindal mentioned,
> > there is not much speed improvement (i guess below
> > 2% not more).
> >
> > I would use gromacs 3.3 cause this is the version
> > with buildin assembly loops,
> > this means much better performance as version 3.2.1
> > on Itanium2 cpus (factor
> > 2 or so overall).
> >
> > >
> > > Thanks
> > > Jo
> > >
> > > Joanne Hanna
> > > Department of Chemistry
> > > University of Warwick
> > > Coventry
> > > CV4 7AL
> > >
> > > J.F.Hanna at warwick.ac.uk
> > >
> > > >>> lindahl at sbc.su.se 11/16/05 15:05 PM >>>
> > >
> > > Hi,
> > >
> > > The intel compilers should support both -O3 (our
> > default when icc is
> > > detected) and -O2. The difference isn't very
> > large, though, since our
> > > assembly loops bypass the compiler on both ia32,
> > X86-64, and ia64 -
> > > but then you need to use gromacs 3.3 or later!!!
> > (3.2 only includes
> > > ia32 assembly loops).
> > >
> > > If you're only having problems when compiling with
> > MPI support the
> > > culprit is likely the mpi wrapper script for the
> > compiler.
> > >
> > > Cheers,
> > >
> > > Erik
> > >
> > > On Nov 16, 2005, at 2:53 PM, Joanne Hanna wrote:
> > > > Hi
> > > >
> > > > I have recently compiled an mpi version of
> > gromacs 3.2.1 with the
> > > > icc compiler. I ran into troubles with this
> > error, at the ./
> > > > configure stage:
> > > > * Sorry, these optimization settings don't seem
> > to work for *
> > > > * your C compiler. Use make CFLAGS=..., or edit
> > the top Makefile. *
> > > > I decided to use the cflags option -O2.
> > > > Can anyone tell me whether this is a good option
> > to use. I
> > > > understand that -O3 enables more aggressive
> > optimisations such as
> > > > loop and memory access transformation. and is
> > recommended for
> > > > applications that have loops with heavy use of
> > float-ing point
> > > > calculations and process large data sets (as
> > from the manual). But
> > > > i don't know which i should use.
> > > > I have been told that optimising too
> > aggressively can produce the
> > > > wrong numbers.
> > > >
> > > > Anu advice would be much appreciated.
> > > >
> > > > Thanks
> > > > Jo
> > > >
> > > >
> > > > Joanne Hanna
> > > > Department of Chemistry
> > > > University of Warwick
> > > > Coventry
> > > > CV4 7AL
> > > >
> > > > J.F.Hanna at warwick.ac.uk
> > > > _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
> > > >
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> > >
> >
> -----------------------------------------------------------
> > > Erik Lindahl <lindahl at sbc.su.se>
> > > Assistant Professor, Stockholm Bioinformatics
> > Center
> > > Stockholm University, SE 106 91 Stockholm
> > > Phone: +46 8 5537 8564 Fax: +46 8 5537 8214
> > >
> >
> > Greetings,
> > Florian
> >
> > --
> >
> ---------------------------------------------------------------------------------------------------
> > Florian Haberl
> > Universitaet Erlangen/Nuernberg
> > Computer-Chemie-Centrum Naegelsbachstr. 25,
> > D-91052 Erlangen
> >
> > Mailto: florian.haberl AT chemie.uni-erlangen.de
> >
> >
> ---------------------------------------------------------------------------------------------------
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Wed, 16 Nov 2005 16:20:04 +0000
> > From: paloureiro at biof.ufrj.br
> > Subject: [gmx-users] order parameter per slice
> > To: gmx-users at gromacs.org
> > Message-ID:
> > <1132158004.437b5c3486353 at webmail.biof.ufrj.br>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Hi!,
> >
> > has anyone used the option -sl in the program
> > g_order?
> > (It calculates the order parameter as a function of
> > the Z-coordiante of the box)
> >
> === message truncated ===
>
>
>
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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