Only if the restrained molecule were to move out of your primary box (it
would then get reimaged). I don't think this would be an issue until you
re-started the simulation (if you kept the same reference structure, of
course).
However, this is unlikely to happen to restrained molecules, so I'm guessing
you'll be fine here. The upside is if anything *does* go wrong, it will go
wrong in a spectacularly noticeable way.
HTH,
Jason
On Thu, Aug 18, 2011 at 8:44 PM, Ozen, Aysegul <Aysegul.Ozen.umassmed.edu>wrote:
> Dear Amber users,
>
> I've been using iwrap=1 in my long simulations as recommended in the Amber
> 10 manual without any issues so far. However, I need to set up a new
> simulation where a subset of residues has to be restrained harmonically in
> the production with respect to the minimized coordinates. I'm restarting at
> every 1 ns and at each restart the reference for the restraint is the same
> minimized structure. My question is would wrapping the coordinates into the
> primary box interfere with the way restraining works? Here's my mdin:
>
>
> &cntrl
>
> iwrap=1, !crd and rst wrapped into a primary box
> irest=1, !restart calculation
> ntx=5, !X and V are read formatted, box info read as
> ntb=2
>
> !constant T
> temp0=300.0,
> ntt=3, gamma_ln=1.0, ig=-1,
>
> !constant P
> ntb=2,
> ntp=1,
>
> !SHAKE
> ntc=2,
> ntf=2,
>
> !restraint
> ntr=1, restraintmask=':1-7,78,144,153,156-160,175-181,186 & .CA',
> restraint_wt=1.0 !kcal/mol/A2
>
> !outputs
> ntpr=500,
> ntwr=50000,
> ntwx=500,
>
>
> nstlim=500000, dt=0.002
>
> &end
> END
>
>
> Thanks!
> Aysegul
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 18 2011 - 18:00:04 PDT
