[gmx-users] Normal Mode Analysis

[Mark Abraham]

On 26/10/2011 7:54 PM, James Starlight wrote:
> 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 ?

We don't know the sense in which it "didn't minimize properly," so 
there's not much point us guessing.

>
> 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)

Whether not PBC represents useful boundary conditions depends on what 
conditions you are trying to model - whether possible periodicity 
artefacts or boundary artefacts are more likely to affect your results.

It does sound like you would benefit from reading some good textbook 
material on molecular simulation :)

Mark

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