> On Apr 29, 2015, at 9:53 AM, Ahmed Ezat <ezat.sci.cu.edu.eg> wrote:
>
> I am sorry but my question is out of this subject.
>
> 5ns windows means dividing the simulation in steps each 5ns or not.
Yes.
> What is meant by this " set ig=-1 here so that the random number seed
> changes automatically on every step otherwise you will get unrealistic
> correlations in your results.”?
This has to do with the well-described “Langevin Synchronization” effect. See it described here: http://www.ncbi.nlm.nih.gov/pubmed/11415160 <http://www.ncbi.nlm.nih.gov/pubmed/11415160> and here: http://pubs.acs.org/doi/abs/10.1021/ct800573m <http://pubs.acs.org/doi/abs/10.1021/ct800573m>
It is also described in the manual (see the descriptions for “ntt=3” and “ig”).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 29 2015 - 07:00:04 PDT
