[gmx-users] Normal mode analysis

[rahul dhakne]

Dear all Gromacs user,

   I am trying to perform the Normal Mode Analysis protein-DNA complex
in vacuum. As the complex is highly negative charge (-163)I performed
the energy minimization of complex in water (to neutralize the
complex). After I get the completely minimized complex, again I have
done energy minimization of complex (in vacuum) for just one step to
get the .trr input file for the Normal mode analysis. As I have to
perform the normal mode analysis in vacuum I did that. But due to
highly negative charge it got stuck in hessian matrix calculation.
Even though it calculate the matrix I got negative eigenvalues after
diagonalizing the matrix.

I also tried with complete energy minimization in vacuum and proceed
for normal mode calculation, but again stuck with the same problem
i.e. high negative charge (-163)

How can I neutralize the system??

or there is any way to do that or probably I am doing something unusual??


Any suggestions will be very welcomed.

Thanking you in advance!

-
Rahul