[gmx-users] Normal Mode Analysis
Mark.Abraham at anu.edu.au
Wed Oct 26 13:34:57 CEST 2011
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 :)
> 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
>> 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.
>> 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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