Thank you for your answer. As Mala said, since it is called the reference
structure, I was thinking that the RMSF was computed with respect to this
structure and not the average structure.
Is there any way with Gromacs to compute RMSF exactly with respect to a
given structure? If I want to study
On 11/29/19 5:53 AM, Mala L Radhakrishnan wrote:
Hi,
I am confused a bit by this answer -- isn't the file specified by -s used
for defining the rmsf (this is what is called the "reference" structure in
the documentation, and I have found that my results do vary using a
different "-s"
Hi,
I am confused a bit by this answer -- isn't the file specified by -s used
for defining the rmsf (this is what is called the "reference" structure in
the documentation, and I have found that my results do vary using a
different "-s" file)...? Or is that just used for fitting and then the
On 11/28/19 12:09 PM, Nicolas Cheron wrote:
Dear all,
I am puzzled by the way RMSF are computed. For a given trajectory (nothing
fancy, just a regular protein):
(1) I have computed RMSF 5 times for two frames i.e. Frame 1/2, 3/4, 5/6,
7/8 and 9/10, each time using the same pdb reference (if
