[gmx-users] Normal Mode Analysis

[Mark Abraham]

On 25/10/2011 3:30 AM, James Starlight wrote:
> I understand this but I've not been able found such information. I 
> dont need in the most accurately  parametries for all cutt-offs of my 
> system but I want to gain inside into the basic cutt- offs worked with 
> the Normal mode analysis.

The cut-offs are particular to the force field, not the manner in which 
the force field is used (EM vs MD vs whatever). There are literature 
references in the GROMACS manual, and also in the published work that 
you have been reading because it has objectives similar to yours. (hint, 
hint)

>
> E.g I've found that PME is not worked here. 

PME does work here. Last time you were apparently mis-matching files...

> So I must to constrain my system with simplest cuttoffs. Could you 
> provide me with the simple example e.g cutt of for interaction beetwen 
> C-alpha atoms only etc?

You can't do that, and shouldn't even if you could.

Mark

>
> James
>
>
>
>     These are particular to the force field involved, not the
>     software. Please consult the appropriate literature, and see what
>     others have used for similar work.
>

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