Thank you for your response. I am running double precision gromacs and I have minimized my structure down to ~1 Fmax, so neither of those concerns should be a problem.
On Thu, Apr 11, 2013 at 12:15 PM, abhijit Kayal <abhijitchemi...@gmail.com>wrote: > > in normal mode analysis you will get 3n vibrational degrees of freedom, > where first 6 should have zero frequency. If some of them are negative that > means that you are in saddle point or your structure is not properly > optimized. So for normal mode analysis you have to be very careful that > your structure is properly optimized. So you have to run gromacs in double > precision. > -- > Abhijit kayal > Research Scholar > Theoritical Chemistry > IIT Kanpur > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
