Hi,
I suspect that the protein doesn't actually break apart - this is a
visual artifact caused by 'wrapping' the coordinates. You can use the
'autoimage' command in cpptraj to re-image your solute back into the
primary cell.
-Dan
On Wed, Jun 12, 2013 at 2:56 PM, Hailin Huang <hailin.huang.my.liu.edu> wrote:
> Dear Amber users,
>
> I am running a prodution simulation of protein 3TNP in a 10A solvatebox.
> After about 25 ns of simlutation time, part of the protein drifts out of
> the solvent box. As the protein falls out further it breaks apart
> eventually and the fragment comes back in from the other side of the
> solvent box. Will I solve this problem by simply increasing the size of the
> solvent box? Is there a way to lock the protein within the box? Thanks for
> any help!
>
> The input file follows
>
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=2000, ntwx=2000, nstlim=2500000,
> dt=0.001, ntt=3, tempi=300,
> temp0=300, gamma_ln=1.0, ig=-1,
> ntp=0, ntc=2, ntf=2, cut=8,
> ntb=1, iwrap=1, ioutfm=1,
> /
>
> Regards,
> Richard
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Jun 12 2013 - 15:00:02 PDT
