Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > Quoting JMandumpal <[EMAIL PROTECTED]>: > > > 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. > > And that's why grompp is complaining. Your cutoff is 1.0 nm, which is half > of > your box size. You said you tried decreasing your cutoff? To what value? > > Also note that -DFLEX_ is not a valid definition, unless you've created it > yourself. What you probably want (from the thread) is -DFLEX_SPC. > > -Justin > > > > > > > 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 > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ========================================
======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
