[gmx-users] Normal Mode Analysis

[James Starlight]

I've found that in general ussage of cutt-offs beetwen 0.8-1.2 nm might
provide good results.

But now I have some problems with minimization of my initial structure

Firstly, I've performed steep minimization ( emtool=1000,  emstep      =
0.01 ) and than CG minimization (emtool=1,  emstep      = 0.001) but as the
result I've obtain that my struucture didnt minimize properly.
Is there any different strategies for the minimization for the ANM ?

In addition I'd like to know about conditions of such normal mode
simulations. Does this procedure require in the PBC ? ( I've performed all
steps including energy minimization in vacuu)


James

2011/10/25 Mark Abraham <Mark.Abraham at anu.edu.au>

>  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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