[gmx-users] Normal mode analysis

[Leandro Bortot]

Hi Rahul,

     Did you make the vacuum minimization with a double-precision version
of gromacs using the L-BFGS algorithm? From the protocol you described it
seems you didn't do it..
     What was the maximum force after the minimization? (check the .log
file)

I hope it helps,
Leandro.



On Sat, Mar 28, 2015 at 7:26 AM, rahul dhakne <rahuldhakne89 at gmail.com>
wrote:

> 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
> --
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