[gmx-users] Using h-angles taking to much time
harpreetsingh05 at hotmail.com
Tue Oct 23 05:25:00 CEST 2007
I am sorry I missed the information.
The problem was while using grompp.
Force field used is g34a1 and operating system is Linux.
> 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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