Jestin, Please don't use all capitals. As Mark has pointed out several times, that's considered shouting. You're probably frustrated that things don't work according to your expectations, but the frustration comes from you not knowing what your doing. Don't blame us for that, go read a manual.
If something is not specified in the .mdp file, the default is used. One thing not specified in your .mdp file is the way to treat PBC, so grompp will want to use xyz. When using (standard) PBC, the cut-off should not be longer than half the box length, as you should be aware if you have read MD basics. Apparently, you're using a cut-off length longer than allowed for your box (says grompp). You say it's 20.1 A to all sides, which should be okay when using a 1.0 nm cut-off. I suspect the last line of your .gro file, which describes the box dimensions, says something else. You should verify that and paste us the last line of the .gro file if you can't see anything wrong with it. Cheers, Tsjerk On 3 Dec 2007 00:19:25 -0000, JMandumpal <[EMAIL PROTECTED]> wrote: > Dear Justin, > > Thanks for the response. > > > This is my input file (em.mdp) which contains parameters for doing energy > minimisation. > > cpp = /lib/cpp > define = -DPOSRES -DFLEX_ > constraints = none > morse = no > integrator = steep > nsteps = 2000 > ; Energy minimizing > emtol = 100 > emstep = 0.00001 > nstcomm = 1 > ns_type = grid > rlist = 1.0 > rcoulomb = 1.0 > rvdw = 1.0 > Tcoupl = no > Pcoupl = no > > > > MY BOX DIMENSION, 20.1* 20.1* 20.1 ANGSTROM. > > > THIS IS THE THREAD WHERE I COLLECTED THE .mdp FILE FOR ENERGY > MINIMISATION. > > http://www.gromacs.org/component/option,com_wrapper/Itemid,84/ > > > > > > regards > Jestin > > > [image: > Shaadi]<http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL > PROTECTED]/1961853_1954773/1961358/1?PARTNER=3&OAS_QUERY=null+target=new+> > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
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