Dear Ross and Jaison,
Thanks for the inputs. Regarding the value for 'ig', I am afraid to say
that all my previous were done with default value for ig and simulations
looked fine for me. Below is the details for MD input I used,
&cntrl
imin = 0, ntx = 5, irest = 1,
ntpr = 100, ntwx = 1000, ntwe = 0, ntwprt=0,
ntc = 2, ntf = 2,
nstlim = 2500000, dt =0.002,iwrap=1,
tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
ntb = 1, ntp = 0, taup = 2.0, pres0 =1.0,
&end
Do I need to worry about anything here? As you see, all my previous MD runs
with protein-in-water were in NVT with ntt=1. What all modifications I
should consider here, while doing microsecond of proteins in membrane?
Many thanks
Regards
Anu
On Wed, Apr 29, 2015 at 2:57 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> > 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
>
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Received on Wed Apr 29 2015 - 08:00:02 PDT
