[gmx-users] How to use different reference structures for g_covar and g_anaeig

Dear All, I have two specific questions: 1.I have been to do COMBINED ESSENTIAL dynamics by concatenating two trajectories. I calcualted the covariance matrix using the default options of g_covar. This should presumably use the average structure for fitting. Now I want to use one of a different

Re: [gmx-users] How to use different reference structures for g_covar and g_anaeig

[EMAIL PROTECTED] wrote: Dear All, I have two specific questions: 1.I have been to do COMBINED ESSENTIAL dynamics by concatenating two trajectories. I calcualted the covariance matrix using the default options of g_covar. This should presumably use the average structure for fitting. Now I want

Re: [gmx-users] How to use different reference structures for g_covar and g_anaeig

Hi Shridhar, g_covar does not use the average structure for fitting. It uses the structure supplied with -s for fitting and from the fitted trajectory calculates the average structure to determine the deviations from. First calculating the average structure and use that for fitting is