[gmx-users] AMBER force constants into GROMOS-96 units

[chandran karunakaran]

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 .

Thanks in advance for your help.

With thanks
Dr.C.Karunakaran


--- gmx-users-request at gromacs.org wrote:

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>    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
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>       (Nathan C. Rockwell)
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>
----------------------------------------------------------------------
> 
> 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
> > > Please don't post (un)subscribe requests to the
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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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