[gmx-users] Normal Mode Analysis

[David van der Spoel]

Den 2019-10-16 kl. 23:31, skrev Adip Jhaveri:
> Hello All,
> I am simulating two proteins in solution and would like to perform Normal
> Mode Analysis on trajectory snapshots.
> 
> I take one particular frame in the trajectory and minimize it, followed by
> mdrun for normal mode analysis. However I am getting constraint errors in
> each of the two steps -
> 1) In minimization it is recommended to use 'cg' method but this does not
> work and it throws an error due to the constraints present in the system.
> 2) I tried using the 'steep' method for minimization but then, during the
> normal mode mdrun, it is giving an error on constraints. How do I solve
> this problem? Do I completely remove the constraints and then perform 'cg'
> minimization and 'nm' mdrun?
Yes.

> 
> Regards,
> Adip
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se