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.abra...@anu.edu.au
<mailto:mark.abra...@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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