Thank you Adrian, really helpful.
Sajeewa
On Wed, Oct 3, 2012 at 9:25 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Hi Sajeewa
>
> I really recommend that you upgrade to amber 12 ! The number of changes
> and improvements are too many to pass on.
>
> You can set ig to whatever you want, as long as it is different every time.
>
> We have scripts to start or restart runs with ig=1 .... N
>
> They all generate independent random streams, uncorrelated. We tested
> this a lot. It makes no difference if you choose ig =1 or 235671 or if
> the igs are consecutive or not.
>
> Adrian
>
>
> On 10/3/12 9:19 AM, Sajeewa Pemasinghe wrote:
> > Thank you Robi. The problem is I am using Amber10 so I don't think ig=-1
> > option is available, that is why I was asking about the specifics of the
> > value for ig.
> >
> > Sajeewa
> >
> > On Wed, Oct 3, 2012 at 5:54 AM, Deák Robert <kokumetto.gmail.com> wrote:
> >
> >> Hi,
> >>
> >> If you don't want to give the value of ig for every individual run, with
> >> "ig=-1" you can set up randomly the seed, calculated from system
> wallclock.
> >>
> >> Best,
> >> Robi
> >>
> >> 2012/10/3 Sajeewa Pemasinghe <sajeewasp.gmail.com>
> >>
> >>> Hi all,
> >>>
> >>> I am running MD of a protein for 20ns. I am going to use Langevin
> >> dynamics
> >>> to fix the temperature. "To avoid synchronization artifacts I have to
> >> set
> >>> a different value for the random seed at every restart." I want to get
> >> the
> >>> above statement clarified a little more. Does that specifically mean
> each
> >>> time my input file says "irest=1", I have to give a different number
> for
> >>> "ig". If so,about the number I give to "ig" does it have a minimum and
> a
> >>> maximum number of digits or can I just give any number as long as it
> was
> >>> not repeated previously?
> >>>
> >>> Thank you
> >>>
> >>> Sajeewa Dewage
> >>> _______________________________________________
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> >>>
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>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
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Received on Wed Oct 03 2012 - 07:00:02 PDT
