[gmx-users] Using h-angles taking to much time

[harpreet singh]

Dear Sir,

I am sorry I missed the information.
The problem was while using grompp.
Force field used is g34a1 and operating system is Linux.

Regards




> Date: Sat, 20 Oct 2007 08:38:19 +0200
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Using h-angles taking to much time
> 
> harpreet singh wrote:
> > 
> > Dear Sir,
> > 
> > I am running Molecular dynamics simulation. Using other constraints the 
> > program is running very fast but if  I am using constraints = h-angles 
> > or all-angles the program is taking too much of time (running since last 
> > 12 hours).
> > 
> > Kindly suggest me that is it the normal behavior of the program or 
> > something went wrong with my data.
> 
> maybe, maybe not. it would have been helpful if you specified that the 
> problem was in grompp.
> 
> which force field are you using?
> which OS and compiler?
> 
> > 
> > Regards
> >  
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> >   -nice    int      0  Set the nicelevel
> >       -[no]v   bool    yes  Be loud and noisy
> >        -time   real     -1  Take frame at or first after this time.
> >          -np    int      1  Generate statusfile for # nodes
> > -[no]shuffle   bool     no  Shuffle molecules over nodes
> >    -[no]sort   bool     no  Sort molecules according to X coordinate
> > -[no]rmvsbds   bool    yes  Remove constant bonded interactions with vi
> >                             sites
> >        -load string         Releative load capacity of each node on a
> >                             parallel machine. Be sure to use quotes aro
> >                             the string, which should contain a number f
> >                             each node
> >     -maxwarn    int     10  Number of warnings after which input proces
> >                             stops
> > -[no]check14   bool     no  Remove 1-4 interactions without Van der Waa
> >   -[no]renum   bool    yes  Renumber atomtypes and minimize number of
> >                             atomtypes
> > 
> > creating statusfile for 1 node...
> > 
> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16#
> > checking input for internal consistency...
> > calling /usr/bin/cpp...
> > processing topology...
> > Generated 279 of the 1225 non-bonded parameter combinations
> > Excluding 3 bonded neighbours for Protein_A 1
> > turning all bonds and H angles into constraints...
> > 
> > 
> > Help yourself to FREE treats served up daily at the Messenger Café. Stop 
> > by today! 
> > <http://www.cafemessenger.com/info/info_sweetstuff2.html?ocid=TXT_TAGLM_OctWLtagline>
> > 
> > 
> > ------------------------------------------------------------------------
> > 
> > _______________________________________________
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> 
> -- 
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> _______________________________________________
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