Hi,
As the references in the manual suggest,
D. J. Sindhikara, S. Kim, A.F. Voter, A. Roitberg,* JCTC*. 5, 1624 (2009) ,
there is a lot of potential for
harm if you don't change ig on restarts or multiple runs. If you already ran
with the same ig,
it may be very difficult to see how bad the effect is, but there definitely
will be some trajectory correlation.
Suffice to say, you should change the ig or use ig=-1 to save you from this
potential pitfall.
--Dan
On Sun, Sep 12, 2010 at 6:44 AM, M. Reza Ganjalikhany <
ganjalikhany.gmail.com> wrote:
> Dear Amber users,
>
> I run MD simulations of a protein in explicit solvent (ntt=3, NPT) the same
> as tutorial #1 section 5 & 6.
> There is nothing mentioned about the value of (ig) in these sections, but
> it
> is mentioned as a necessary value (ig=-1 or random value) to be set for
> ntt=2 or 3 in the users' manual.
>
> Does it make significant differences in the final results if default
> (71277) is set instead of random values (ig=-1)?
> Is it necessary to set *ig* to random values during all the MD simulation
> steps whenever ntt=3 is used?
>
> Any comments would be helpful,
>
> Regards,
> M. Reza
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>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Sat Sep 11 2010 - 15:30:03 PDT
