[gmx-users] Re:

Bryan Roessler roessler at uab.edu
Thu Apr 11 19:29:14 CEST 2013

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
<abhijitchemiitd at 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

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