[gmx-users] ED sampling and overall rotation
stockner at ucalgary.ca
Fri May 13 16:58:02 CEST 2005
thanks for your answer. One more thing is unclear.
The eigenvectors used for enhanced sampling define directions in space.
During a simulation, my protein will move and tumble and the initial
orientation will not match with the orientation at a later time point of
How is this overall rotation of my molecule taken into account when
projecting the MD step onto the subspace spanned by the eigenvectors
that are used for enhances sampling?
University of Calgary
Department of Biological Sciences, Biol 416
2500 University Dr
Calgary, AB, T2N 1N4
Email:stockner at ucalgary.ca
>Thomas Stockner wrote:
>>Dear Gromacs users,
>>I am trying to use ED sampling, but some details remain unclear.
>>How is the parameter "slope" (nm/step), specified with make_edi, exactly
>>calculated (defined)? Is it an average over the last X steps?
>it's a running average over the last 500 steps (usually ps).
>>Are bond constraints (LINCS) applied after atoms (e.g. CA) are projected
>>along the eigenvectors in case of rejection of the MD step?
>edsam is called after lincs (or shake), as an additional coordinate constraint.
>no MD step is "rejected" btw. edsam either accepts a step as is, or it corrects
>the position along selected eigenvectors, if required.
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